Mass Effect 4: Indoctrination Theory

Like a lot of fans of Mass Effect, I was a bit weirded out by the end of the series. I wouldn’t say that I was “butthurt” per se, but the “three doors” option did seem to fall short of the series’ potential. But when I found out about Indoctrination Theory, I was immediately thrown off the toilet and my head smashed into the proverbial bathroom sink. I became obsessed by the possibility that not only was the ending to the series one of the best endings of all time, but it was also one of the darkest and most heartbreaking endings imaginable.

For those of you who don’t know anything about Indoctrination Theory, check this out

So I’ve written my own outline for a new Mass Effect game that takes into account the idea that Indoctrination Theory is true. The war against the reapers is far from over. I call this project…


 … not only as a nod to fans who speculate about this theory, but also because the conflict following the Battle of London closely follows the theme of the importance, and danger, of indoctrination.

In this project I refer to Shepard as she because my version of Shepard looks like this:


And, believe it or not, the protagonist of ME4 is none other than Major Coats. That’s right, this guy right here:

Major Freaking Coats

Major Freaking Coats

He’s even the guy seen in the original teaser trailer!

Contents of Proposal

Section 1: Themes

Section 2: Cast of Characters

Section 3: Story Outline

Section 4: Concerns, Questions, and Extra Details



Indoctrination will be one of the main themes of the game. The tantalizing hints lurking in the background of the original trilogy will now be in the forefront. Story-wise, the conflict against the reapers changes in the two years following the failed Battle of London. Suspicions will run high among the new crew of heroes as well as in society in general. The main team will be tightly-knit, but they will always be on the lookout for signs indoctrination in the team. There will even be instances when the player will have to execute members of his own crew, or at least test them to make sure they still have their free will. No one will be above suspicion. (Think John Carpenter’s The Thing.)

Femshep 5

 Hope will be a major theme. After the galaxy united against the reapers and subsequently lost the final battle, the harvest began in earnest. ME4 will have a much darker tone than the original trilogy, but no matter how dark things get, Coats and his crew hold on to hope. Much of that hope is born from Shepard’s example and the actions she took. To those who refuse to give up hope, Shepard truly is a legend. 

Totally, totally hopeful.

Totally, totally hopeful.

Another theme: Science won’t save us. The Crucible, a scientific project of much vaster scope than the Manhattan Project, failed utterly. According to Indoctrination Theory, Shepard’s dream and the options of either union with machines or control of machines were folly, nothing more than variations of different kinds of failure. Reapers themselves, the end result of scientific development, are merely apex predators and cultural bureaucrats. In ME4, only strength of will can save sentient, organic life. This theme will, of course, be emotionally and intellectually challenging for the fans of Mass Effect (or fans of science fiction in general, for that matter).

 leviathan me3

The leviathans will be major players in this game. They can indoctrinate just like their creations, the reapers, and when the reapers destroy the fleet that Shepard put together, the reapers will see the leviathans as their most dangerous opponent. Major Coats will become their greatest ally as the true war against the reapers begins, despite the fact that the leviathans are not really trustworthy allies at all. In fact, they remain much more interesting as monstrous beings intent on survival. They are incredibly pissed off about the fact that Shepard dragged them into conflict with the reapers.

Also, the Catalyst, when attached to the Crucible, is a device that amplifies indoctrination signals. It does nothing but this, and the purpose and interior shown at the end of ME3 were only a part of Shepard’s indoctrination dream.



"Two million dead in the first day..."

“Two million dead in the first day…”

Major Coats / Commander Coats

Species/Gender: Human male.

Class: Player choice.

Coats is the protagonist controlled by the player. He was one of Admiral Anderson’s best soldiers during the London operations, and he becomes the team leader of a mixed-species guerrilla band during the events of ME4. The player can choose his class, and after the second chapter of the game the player can modify his appearance (hair, facial hair, tattoos, scars, etc).

Barla Von

Species/Gender: Volus male.

Class: Non-playable character.

Barla Von is the information broker seen working on the Citadel in ME1 and ME3. Once Coats and his rag-tag group board the Vengeance and accept his offer, Barla Von becomes the team’s “boss”. He is in charge of financing, gathering supplies and intel, and he plans operations for the team until Commander Coats takes over that role.

He would, of course, wear a cooler suit than this.

He would, of course, wear a cooler suit than this.

Thresher” Toombs

Species/Gender: Human male.

Class: Soldier with strange, unique enhancements. Listed as Mercenary.

Known as Corporal Toombs in ME1, he is a survivor of the Akuze Thresher Maw incident, escaped from cruel experimentation by Cerberus (including being injected with Thresher Maw acid), and later becomes a mercenary leader. If Shepard shot him in ME1, then Toombs survived; even if he shot himself, he somehow survived and put his life back together. Toombs is partly insane, but his will to survive and independent spirit have made him a force to be reckoned with. He meets Coats during the escape from London and eventually becomes his best friend. Toombs wears unique mercenary armor and has grown his hair out not unlike Snake Pliskin. Unlike everyone else on the team, he has no love for Shepard (unless she killed or let Toombs kill the Cerberus scientist in ME1).

Toombs way back in the first Mass Effect.

Toombs way back in the first Mass Effect.

"Thresher" Toombs after a makeover.

“Thresher” Toombs after a makeover.

Yluvia Tuvoss

Species/Gender: Asari.

Class: Vanguard. Listed as Huntress.

This huntress has skin so dark that she is nearly purple. Her mother is an asari and her father is a hanar (the same hanar that Lanok serves). She is very cultured and likes to talk to (or educate) Coats on the works of art produced by the various sentient species. She has no scientific training like Liara, nor the unyielding principles of Samara; she is just a siari practitioner willing to fight to protect the cultures of all species.

Asari Biotic by sammael89 on deviantart.

Asari Biotic by sammael89 on deviantart.

Lanok Tuvoss

Species/Gender: Drell male.

Class: Sentinel. Listed as Enforcer.

This enforcer for the hanar has reddish-pink skin tones with purple highlights and blue-green gills. This extremely hot-blooded drell often vows to do anything to protect his teammates, but is also the first to demand an execution anytime someone is suspected of being indoctrinated. He is a long-time friend of Yluvia due to working for her hanar father. He has even taken Yluvia’s last name because her father effectively “adopted” him.

Back of a Drell's Head by alarielle88 on deviantart.

Back of a Drell’s Head by alarielle88 on deviantart.

Janerel Pazness

Species/Gender: Batarian male.

Class: Biotic adept. Listed as Barbarian Monk or simply Monk.

The nephew of outspoken Governor Pazness, a war asset from ME3 who told his people the truth about the reaper invasion. Janerel was born into a high caste family. He is not a typical batarian pirate or mercenary; instead, he is a devout believer in his peaceful religion and, after the fall of Kar’Shan and the destruction of London, he is the best his people have to offer. Even though he is a good and decent person, like other batarians he is an advocate for slavery, which will make for some interesting conversations with Coats.

Batarians doing what they do. Total North Korea style.

Batarians doing what they do. Total North Korea style.

Dreelo “Salamander” Daelor

Species/Gender: Salarian male.

Class: Soldier. Listed as a Sniper.

This green-tinted university dropout constantly lies about the many scientific achievements he helped pioneer. He’s a good tactician and a damned good soldier, but he always wanted to be a great thinker. He wears a short robe over his armor, which is a tradition in his family. He was nicknamed Salamander by a human comrade he met in London.

salarian attitude


Gloria Bellicosa

Species/Gender: Human female.

Class: Soldier. Listed as Heavy Assault.

This white-haired, blue lipstick-wearing Alliance marine soon becomes a devout disciple of The Shepherd, which is the belief that Commander Shepard was a legendary figure whose alleged death during the failed Battle of London will somehow give all organic life the strength to overthrow the reapers. Her devotion is single-minded, almost fanatical. Despite her small size, she is very, very strong. Firing big guns and blowing up big bombs is her specialty. She is one of the main characters who challenges Coats with the idea that science cannot save us.

Sik Vraneth

Species/Gender: Raloi female.

Class: Infiltrator. Listed as Rebel.

Mentioned only briefly in Mass Effect mythology, the raloi are an avian species who withdrew from the greater galactic community and destroyed their satellites in order to appear technologically pre-spaceflight and thus non-threatening to the reapers. Sik (pronounced “seek”) believes this is foolish, and she joins Coats’s crew in the second chapter. She wears a protective suit, as do most of her people when they go off-planet, but this is a cultural tradition having to do with isolationism rather than an immune-system imperative like with the quarians. Her suit is dark and gives her a very “ninja” appearance. The raloi are descended from birds, but in order to avoid awkward wings and goofy-looking feathers, Sik looks more like a turian/quarian combo. Her dark mask sort of looks like an evil version of Ultraman, thus giving her a “death zen” look. Despite her high-tech trappings, she wears necklaces and bracelets decorated with feathers or a feather-like material.

Mirtis Arthenn

Species/Gender: Robot. Shackled AI created by the extinct arthenn species.

Class: Engineer. Listed as Corpse Guardian.

Mirtis, whose name means “death” in Lithuanian, was created by the arthenn many cycles ago in order to 1) protect the graves of the dead from being disturbed and 2) protect the living from the reapers. He was made in the shape of the arthenn, much the way EDI appears human. He was never cryogenically frozen (thus avoiding the “Let’s thaw him out!” theme of Javik), but has rebuilt himself over and over again. His empty, decommissioned bodies can be seen near his lair, dozens stacked one on top of another. Other robots were given the same task as Mirtis, but only Mirtis was strong-willed enough to avoid being indoctrinated during this cycle.

Eight playable companions can join Coats’s team. There is one of every basic class available, except for soldier, of which there are three. However, each soldier has his own unique specialization; none are truly vanilla soldiers. There are three females, one robot, and four males.

As for enemies, there are three main villains, two of which have been seen in previous Mass Effect games.


The first reaper. He is the most powerful and malevolent of them all. When the Great Library is destroyed in chapter eight and the reapers are unsure how to proceed, Harbinger argues that the destruction of all organic lifeforms must continue, which Magnus opposes.


The second-oldest reaper, and perhaps the wisest, is in charge of recording the cultural achievements (or “memetic information”) of every culture being harvested in this cycle. He took a special interest in Shepard and did most of the work during her subtle indoctrination (which is why he chose to arm Shepard with a Carnifex handgun, which has his name, Magnus, written on the side). When the Great Library is destroyed, he argues that the harvest should be ended and other options explored. He is nowhere near as bloodthirsty as Harbinger.

Check it out. During the indoctrination dream sequence, Magnus gave Shepard a Carnifex heavy pistol... which has his name on the Side! Magnus is a subtle monster with a touch of class, unlike Harbinger.

Check it out. During the indoctrination dream sequence, Magnus gave Shepard a Carnifex heavy pistol… which has his name on the side! Magnus is a subtle monster with a touch of class, unlike Harbinger.

Pope Harper

Formerly known as the Illusive Man, Pope Harper is the head of the establishment church that is formed during the two year interim following the opening chapters of the game. According to the Church of the Ultimate Synthesis, the reapers are gods who came to bring peace to the various species of the galaxy, and the destruction they wrought was only a result of their war against a galaxy-wide cabal who sought to enslave everyone. His musical theme is the same as the original Illusive Man theme, but possibly augmented by creepy church organs.

Start out with this...

The Illusive Man becomes…

pope harper aka illusive man

… something like THIS.


Chapter One: The Flight from Earth

Mass Effect 4 opens with a cinematic showing the united galaxy’s failed attack on the reapers surrounding Earth. While the Hammer team prepares to move, Coats says, by way of narration, “I was there. I was there when Shepard fell.” The Hammer team rushes the beam but are annihilated by Harbinger. Shepard is blasted and assumed dead (and if the ME3 player did not see Shepard “breathe” and have a high EMS score, then Shepard did truly die after being indoctrinated by Harbinger with assistance from Magnus). The reapers surround the portal and Major Coats gives the order to retreat. He is haunted by this decision for most of the game.

Admiral Hackett brings the Catalyst near the Crucible, but because the arms of the Citadel are never opened, he and most of the other space-based Sword and Shield teams are surrounded and wiped out. All hope of victory is lost. While Anderson remains in London to coordinate a general retreat and long-term guerrilla struggle, he orders Major Coats to find a ship, retreat, and gather reinforcements. Major Coats argues that there’s nothing they can do: The fleet is lost, Shepard is dead, and the union of galactic civilizations is at an end. Anderson argues that they have no other options and Coats must leave. “I can fight a losing war here on my own,” says Anderson. “I don’t need your help for that.”

Major Coats reluctantly agrees and makes his way through ravaged London. His generic marines fall one by one, but Coats meets six of his teammates while en route to a grounded ship hidden in the countryside. With news of the fleet’s destruction and Shepard’s crew fleeing, Coats and his team board the cramped shuttle and flee from Earth.


Chapter Two: The Dead Planet

Seeking temporary shelter in a sparsely populated system, Coats picks up a distress signal on Klencory and decides to give aid in exchange for supplies. They find volus billionaire Kumun Shol living on his own private excavation site / wealthy resort / religious commune. He is surrounded by believers obsessed with Shol’s “beings of light” theory. Shol is more than happy to tell Coats about these imaginary beings who will destroy the reapers. In fact, he is not surprised that the galactic fleet failed. He also has many mercenaries on hand, plus several odd scientific enterprises spearheaded by raloi, the avian species living in self-imposed exile. (Klencory’s cult-atmosphere is not unlike modern Scientology.) Barla Von and his team of vorcha are also working on a project of their own. Barla is much less genial than Shol.

The raloi tell Coats that several people have disappeared deep in the excavation site and no search teams have found them. Coats and his team descend and find a labyrinthine crypt built by the arthenn, a sentient species that went extinct 300,000 years ago. The crypts are defended by robots designed to look like the arthenn, their creators.

When they are deep underground, they are contacted by Barla Von. He claims that nearly everyone on Klencory has been indoctrinated. Many clues show that Klencory is the birthing place of the new religion that will help the reapers harvest more organics; it is always a necessary stage in the harvest to create one or more prophets who then milk the rich and harvest the poor. Barla Von says that he fell in with Kumun Shol when he decided to use procured Normandy stealth drive blueprints to create a new ship after the destruction of the first Normandy. He has faced many obstacles and thought he could use Shol’s wealth and volus family connections, but he now regrets trusting Shol. Barla Von used raloi engineers because he wanted the project to remain in absolute secrecy, and few information brokers keep their eyes on the raloi. Barla Von makes a deal with Coats: If he’s a good enough soldier to escape from Kumun Shol’s insane death trap, then he’s good enough to take Barla Von’s new ship… the Vengeance.

Coats meets the last two members of his team: Sik the raloi and Mirtis the arthenn robot. Sik joins because she is ashamed of the choice of her people and wants to do what she can to fight the reapers. Mirtis joins because he is programmed to defend the graves of his masters. Now that his comrades have been indoctrinated or killed, he cannot do it alone and must fight those responsible for this outrage: The reapers.

The crew fight their way out and Barla Von and his vorcha crew pick them up in the Vengeance. The roster is now complete, and they decide to use the stealth ship to conduct guerrilla raids on the reapers. The Vengeance looks like a small, dilapidated “trailer park” version of the Normandy, but the stealth drive works perfectly.


Chapter Three: There Is No War, Only the Harvest

Two or three years pass. We see the pathetic state of the galaxy as Coats and his team perform guerrilla raids and small rescue missions. The leaders of many worlds are indoctrinated and the message is spread that the reapers are actually the friends of all sentient life. A great deal of propaganda explains that they were merely wiping out a galaxy-wide cabal of conspirators who were plotting to enslave the galaxy. One by one the great civilizations of the galaxy fall to the reapers. Massive harvesting operations are conducted, and only small teams of guerrillas willing to quickly flee have any chance of survival.

Cerberus changes its role and becomes more like a militant church that helps gather people for indoctrination or eradication. The Illusive Man comes out of the shadows and becomes Pope Harper, a prophet of the “reaper saviors”. The dogma of Cerberus stands in opposition to the new underground spiritual belief that venerates Shepard as a saint or even a messiah. Shepard is often referred to as The Shepherd (sic).

Through side missions, we see Barla Von become a boss in every sense of the word while Coats takes the title Commander and remains in charge of ground operations. Barla Von uses his information brokering skills to amass a great deal of information about indoctrination.

At this point, the Vengeance can be upgraded. The player can even tailor the interior to his or her own taste with themes like Space Viking, Cyber-Goth, Clean and Modern, High-Tech Neon, Warm and Cozy, and Religious Nutjob (which has Shepard relics everywhere).


Chapter Four: The Oath of Death

After a few missions that produce little to no results against the triumphant reapers, one of the crew members points out that they are simply not as powerful as Shepard’s legendary crew, and Coats is certainly no Shepard. What can they possibly do against the reapers, seeing as Shepard failed and there is no longer a fleet to challenge the reapers?

Commander Coats rallies the team with this idea: The old alliance didn’t understand the power of indoctrination, how it works, and how subtle it can be. Force of arms never had a chance to defeat the reapers, as evidenced by the failed operation to retake Earth. But Coats and his team have learned a lot about indoctrination in the past two years; they are armed with an understanding that Shepard lacked. Commander Coats says that his team will stand together under her example, but they will also take a Death Oath, which says that the mission to destroy the reapers is more important than any of their individual lives, and if one of them falls under indoctrination, the others will honor their friendship by executing them immediately.

The Oath marks a turning point in this ragtag group’s war against the reapers.


Chapter Five: The Blood of Heroes

Through a series of cinematics (via intel gained by Barla Von) we find out that Shepard’s old crew has attacked an important reaper facility. If Garrus is still alive, then of course he leads the assault.

During the operation, one by one most of Shepard’s old crew is killed. Unfortunately they find out that the Mu relay has been moved inside the Citadel itself, thus making the source of the reapers’ enhanced indoctrination signal seemingly impregnable. Furthermore, much of Shepard’s crew’s intel seems to have overstated the importance of their target: The only data they retrieve before escaping is the location of something the reapers call the Great Library. The Great Library is where they store every available piece of information about the cultures of the current cycle before those cultures are destroyed. The Great Library preserves the information before it can finally be absorbed by each reaper near the end of their harvest and their return to dark space. Disappointed, the team transmits the information to a few trustworthy guerrilla teams.

Barla Von, information broker that he is, finds the information and notes the location of the Great Library. He and Coats and the rest of the crew debate the importance of the intel.


Chapter Six: A Deal with the Leviathans

Using their information on Shepard’s old operations, Commander Coats makes a plan to find the leviathans, who have been forced to move from their old hideout due to reaper attacks. They find them and learn about their ability to indoctrinate. Coats negotiates with their leader and argues that he himself should not be indoctrinated, as the leviathans already have plenty of indoctrinated muscle and Coats is a more powerful ally when he is in control of himself. The leviathans grudgingly agree. Coats presses the leviathans on how they could let their reapers get out of hand, and the leviathans admit that they had planned for that eventuality but the revolt of the reapers happened too quickly. They tell Coats that the Citadel/Catalyst combination was designed to kill, overpower, or reprogram their synthetic creations, or even any synthetic creation at all. This is the first cycle in which the Catalyst was ever finished, but unfortunately the reapers are only using it to strengthen their own indoctrination signals.

The leviathans never completed a Catalyst of their own because of the danger of having it fall into enemy hands. They ruled the galaxy for untold millennia without need of a Catalyst, and they suspect that the reapers are only using the Catalyst/Citadel combination now because their numbers were so drastically reduced during the Battle of London. It seemed to be the only way to indoctrinate enough worlds in time to bring their harvest back on schedule. Still, with the Mu relay hidden and the Citadel covered with reaper forces, it seems the reapers are in no danger of having the Catalyst used against them.

More discussions are had, and eventually the importance of the Great Library is revealed. Since it is the key to recording the cultural data of every sentient species, destroying it would undermine the reapers’ mission to “preserve” the cultural advancement of every species in this cycle. The leviathans are not sure how their creations would react to the destruction of the Library, as it has been a long time since they were originally programmed, but they reason that this will at least throw them into disarray – and, in a best-case scenario, shut them down. The leviathans have survived until now by hiding from their monstrous creation, but now that Shepard has revealed their presence and placed them all in danger, they agree to help Coats in his personal war against the reapers.


Chapter Seven: The Leader of the Resistance

Coats learns from the leviathans that the teleportation beam placed in London two years ago was nothing but a red herring set by the reapers in order to give the united galaxy some hope of victory. It did its job of drawing the enemies of the reapers into one place, thus making it possible for them to be destroyed. Coats is reminded of the shame he felt for calling a retreat, but he realizes that he actually made the right decision. This realization gives him new-found strength. It’s a paradigm shift in how he sees the world.

News comes that Admiral Anderson has been killed by one of his own soldiers – an indoctrinated sleeper agent – and the resistance on Earth effectively ends. The news is so devastating that Barla Von succumbs to indoctrination. The crew notice him acting strangely, and Coats is forced to restrain him and interrogate him. Whether he is executed in accordance with the Death Oath or is released and forces the player to kill him later, Commander Coats becomes, in some sense, the “leader” of the resistance against the reapers.


Chapter Eight: The Destruction of the Great Library

Commander Coats contacts the remnants of Shepard’s crew and together they plan an operation to destroy the Great Library. The Vengeance and the Normandy fly to Ploba, a gas giant which hides a massive facility used during each harvest cycle to record cultural “memetic” information before it is distributed to each reaper before they return to dark space. (By this time the Vengeance has already been outfitted with plating strong enough to withstand the pressure of Ploba.)

The mission is incredibly difficult. The reaper presence is strong. Not only is the Normandy destroyed while distracting several reapers, but one by one the rest of Shepard’s old crew are killed while completing their part of the mission. One or more of Coats’s crew are either killed or indoctrinated (and must be executed). But the mission is a success: The Great Library is destroyed and Coats and the rest of his crew escape in the Vengeance.

The destruction of the Library throws the reapers into complete disarray. This has never occurred during any cycle. A schism develops between Harbinger and Magnus. Harbinger declares that the destruction of organics and recording of their genetic structure must continue. Magnus argues that recording genetic information is useless without a complete record of cultural memetic information, and thus they have failed in their purpose and must return to dark space. The reapers are not sure how to continue.


Chapter Nine: Hunt Them Down

The location of the leviathans and their role in the destruction of the Library is discovered by the reapers. As Commander Coats and his crew return to bring them news, they find the reapers assaulting the planet in force. Coats and his team barely escape from the terrible, planet-shattering assault.

During the escape, the peaceful vorcha crew of the Vengeance are indoctrinated and attack Coats and his team. They must be killed and Toombs will have to pilot the ship during the final assault.


Chapter Ten: The Citadel and the Catalyst

Though the leviathans have been destroyed and can no longer act as a powerful ally against the reapers, Commander Coats realizes that the reaper assault on the leviathans took a great deal of their manpower away from defending the Citadel and the Catalyst, which have been brought together to broadcast their amplified indoctrination signal. The team will never see another chance like this, so Commander Coats leads his crew on a suicidal assault onto the Citadel/Catalyst.

Fortunately Coats has already upgraded the Vengeance with an ultra-hard plating around the very front. He never believed that the Citadel was truly impregnable even with its arms closed. The Vengeance tears through like a syringe, but is destroyed in the process.


Chapter Eleven: The Fate of Commander Shepard

The Citadel’s architecture now looks nightmarish. In some sense the reapers revere organics because they are programmed to record all aspects of life during their harvest, but they are also envious of organics – and this hatred is displayed in the Citadel’s horrific surroundings. As Coats and his crew fight their way to the Catalyst connection, the few remaining guardian reapers tear up their surroundings in a desperate bid to kill them. Several members of the crew are either killed or indoctrinated and executed. The survivors find a chamber that looks like a cathedral bathed in golden light… and there, they meet Commander Shepard.

The fate of Shepard depends on the player’s choices in Mass Effect 3. In accordance with Indoctrination Theory, if Shepard chose (during the hallucinatory ending) either Synthesis or Control, then Coats will find her body in the frozen cathedral. It has been enshrined by the reapers because they respect the fact that she was the most dangerous opponent they ever faced. The scene will be very sad, and Coats will burn the body to hide the fact that she was indoctrinated and as a sign of respect and to “send her on to a better place.” If the player was able to avoid indoctrination at the end of ME3, then they meet Shepard alive. After the Battle of London the reapers recovered Shepard’s broken body and kept her alive but imprisoned on the Citadel/Catalyst. Shepard can no longer move very well and is effectively kept alive by machines. The reapers ceased trying to indoctrinate her in a strange show of respect. When Coats and his team talk to her, they find out that, miraculously, her will is still strong. She tells the team to never, ever give up. This strengthens the team and helps them avoid indoctrination. Shepard then unhooks herself from the machines keeping her alive and does some amazing, balls-out suicidal stuff that ends up destroying one of the reapers who returns to stop Coats and gives his team some breathing room during the final mission.

The survivors finally reach the Catalyst broadcast chamber and upload a program developed by the leviathans. The reapers’ own indoctrination broadcast is turned against them. All synthetics and indoctrinated organics turn against their former masters. Even the smaller destroyer-class reapers are given new orders: Kill the reapers.

A great civil war erupts, and many of the strongest, oldest reapers are destroyed. Any land-based reapers are overwhelmed or forced into space by legions of ground-based indoctrinated forces, while reaper capital ships in space find themselves assaulted by newly-indoctrinated reaper destroyer-class ships. Seeing an opening, the fighting spirit is reawakened in many organics, who quickly turn on the ancient tyrants.


Chapter Twelve: Harbinger

The last of the reapers converge on the Citadel in order to stop Coats. They are hounded by their own kind and the Citadel becomes an incredible battleground full of reapers killing reapers. Magnus is strangely absent, but Harbinger broadcasts such a powerful indoctrination signal that much of this part of the game becomes dreamlike and surreal. Finally only Harbinger remains, and he destroys the Presidium tower (where Coats and his crew were defending the new broadcast signal). Only Commander Coats and “Thresher” Toombs survive this onslaught, but they manage to actually land on Harbinger’s hull and force their way inside.

In a nightmarish and constantly changing landscape, the two friends manage to kill all of Harbinger’s internal defense forces. There they meet Pope Harper, formerly known as the Illusive Man. He is a shell of his former self, and Toombs finally has his revenge by beating the piss out of him with his bare hands. Now without weapons, Harbinger flies toward the sun in an effort to roast the heroes alive. Unfortunately Toombs is then indoctrinated, and in an incredibly sad “final boss” battle Coats is forced to kill his best friend.

Coats uses the last of his strength to destroy Harbinger’s brain. As the corpse of the reaper still flies toward the sun on momentum alone, Coats sits broken and bleeding and listens to transmissions about the galaxy’s inhabitants destroying the last of the reapers, and how the indoctrinated forces are simply falling dead on all worlds because they no longer have any masters to tell them what to do. Coats watches the sun approaching, prepares to die, and thanks Shepard for all that she did.

Magnus, the last surviving reaper, flies in and retrieves the flaming corpse of Harbinger. Coats is brought back to Earth. On a beautiful green field with Harbinger’s corpse burning nearby, Coats speaks with Magnus. Magnus explains that the cycle has been broken; it was broken by Shepard years ago, but Harbinger was too stuck in his ways to understand that. He says that it’s up to Coats and the rest of organic life to find a new way now that the cycle is over. Coats gains Magnus’s promise of non-hostility, and then the rebuilding begins all across the galaxy.


The End

The cycle of synthetics destroying organic life (the created turning on their creators) is, for a while at least, thwarted by a new belief system that has Shepard as its head or “messiah” figure. The new belief system enshrines the unique force of will exhibited by organic life. The urge to create synthetic life becomes taboo. Coats, now hailed as a hero, tries to live a simple life but becomes a reluctant prophet of this belief system. Sentient organic species look forward to a chaotic future in which do what thou will, not what thou are programmed to do, becomes the whole of the law.

Magnus departs with a terrifying shriek and claims he won't start a shit-storm elsewhere.

Magnus departs with a terrifying shriek and claims he won’t start a shit-storm elsewhere.


What sort of enemies will the player fight?

Commander Coats and his crew are much less powerful than Shepard and her legendary teammates. They won’t have to take on waves of Brutes and Marauders, though, because those were only important during the initial battle to control the galaxy. During Coats’s time, indoctrination is the tool of choice for the harvest. That, combined with the darker tone of ME4, means that the player will mostly be fighting extremely creepy looking enemies who retain the same shape as their parent species. Dark asari biotics, krogan heavy asault units, turian snipers with glowing eyes, etc.

What kind of equipment will they use?

Commander Coats’s boss Barla Von doesn’t have access to the array of gear available to Shepard. Raided caches of enemy supplies will help the crew out, but overall their gear will be much less “fancy” than in previous ME games. This is not only due to the desperate tone of ME4, but is also key to the new theme of “science won’t save us.”

What about a female protagonist? Isn’t the Mass Effect series about player choice?

As a player who always uses a female Shepard, I understand this concern completely. The solution is simple. At the beginning of the game, the player can either select the male Major Alexander Coats or his sister, Corporal Valerie Coats. Valerie is an alliance marine who also finds herself in London during the final battle of ME3. When the battle is lost, she accompanies her brother when Anderson orders him to flee and find reinforcements. When he is killed en route to the ship, he gives his sister a battlefield promotion to Major. That way dialogue can refer to Major Coats without a lot of rewriting based on gender. Also, two years pass after the flight from Klencory; at that point the player can select from a number of hair styles, hair color, makeup, scars, tattoos, and perhaps even skin tone adjustments.

Why go with Commander Coats as the protagonist? Isn’t the Mass Effect series about Commander Shepard? How can Mass Effect 4 not have Shepard as the protagonist?

I originally had the idea to make Coats the protagonist because I just finished reading The Hobbit a few weeks beforehand. In The Hobbit, a badass named Bard is introduced near the end, and he does some badass stuff that the protagonist could never do on his own. When I met Coats near the end of ME3, I was intrigued by the idea that there was a hero fighting his own personal battle in his own corner of the ME universe. Finding out that he was the character shown in the original teaser trailer nailed it for me: In a bleak world where indoctrination is the ultimate power and heroes can die at any time, Coats was the perfect, grim fighter for a war against an enemy that not even the galaxy’s strongest soldier could overcome. And I’m not the only one who has had this idea, as one of the online Indoctrination Theory videos even suggests making Coats the protagonist of another Mass Effect game!

I also think a change in protagonist is good for the series because franchises need to be shaken up. It’s natural to become comfortable with things as they are. It’s natural to think that ME4 should be about Shepard and her love interest saving the day and then holding hands while the sun sets behind them, but sometimes what the audience wants isn’t necessarily what they “need”. We need to see radical and shocking changes in order to avoid boredom that can set in even with the best of franchises. Plus doing something shocking with the former protagonist will only lend weight to the idea that the player is facing the greatest threat that the galaxy has ever faced. If Shepard is not safe, then no one is.

So just what is the Catalyst?

The Catalyst, which has never been finished until this cycle, was supposed to be a way for the leviathans to control their reapers if they ever went nuts-balls. Leviathans don’t make anything on their own; their entire culture is based on manipulating other lifeforms. Many times they witnessed organic lifeforms overcome by their own creations. The leviathans created first Harbinger, then Magnus, to chronicle the lives and deaths of other sentient species in order to preserve them. Fearing that their growing reaper forces could get out of control, they devised a machine to strengthen their own indoctrination signal so they could immediately put a stop to the reapers if they had to. Of course, once it is made, a tool that powerful could be taken and used against the establishment. The leviathan rulers had ruled for so long that they saw no sense in creating something that could potentially be used against them. They wanted to enjoy their rule, not worry over how to protect a device that they had lived well enough without for millions of years.

The reapers turned on their creators so quickly that they never had time to build the Catalyst. Only a few leviathans escaped the freezing wrath of the reapers. They lived in exile and while some considered making the Catalyst in order to regain control of their creations, most of the exiled leviathans argued that that would only put them at risk. The gamble was too great, and they had to give up their old empire in order to avoid complete extinction. In the end, only hiding from the reapers and their endless cycles was the sure path to survival. The Catalyst was simply too powerful; there was not even any guarantee that one of the surviving leviathans wouldn’t simply enslave all the others.

For the purposes of Mass Effect 4, it is assumed that the Catalyst and its functions, as shown in ME3, were only a part of the indoctrination dream sequence constructed by Harbinger and Magnus. Even the reapers considered destroying the Catalyst, but after they lost so many during the Battle of London, they decided to keep it and use it to boost their indoctrination signals and put their harvest back on schedule.

In the end, the Catalyst was a scientific tool and weapon of such power that it was the doom of both the leviathans and the reapers.

*     *     *

Hey readers! If you liked this post, you should check out some of my books. I’ve got an epic series called Demonworld, which is equal parts Mad Max and Lord of the Rings (think “science fantasy”), and a much-loved gamebook series called Heavy Metal Thunder which is currently a hyperlinked Kindle book but will be a fancy phone app any day now.

6 responses to “Mass Effect 4: Indoctrination Theory

  1. Pingback: Mass Effect 4: Indoctrination Theory | kylebstiff

  2. Pingback: Some Ridonkulous Mass Effect Fan Fiction | kylebstiff

  3. So some people read a version of this outline on the clevernoob forum and said that one problem with my ME4 idea is that it undermines or tosses out player choices made in the first three games. I never really intended that, but I can see how they came to that conclusion. This was my response.

    One reason why it might seem that way is because this outline focuses on necessary missions and ignores side missions and population centers that have lots of character interaction. It’s sort of like how whether or not you choose to let the council die in ME1, you still have to go to Mars at the beginning of ME3; whether or not you kill Wrex in ME1, you still have to take Grunt to see clan Urdnot in ME2. There are lots of different paths, but all those paths lead to one end goal. Now, if you take Indoctrination Theory seriously at all, then you also might start to think that many choices are illusory. At the end of ME3 it looks like Shepard can do this, or this, or even that, but in reality she can really only do one thing, and that’s the mission she originally set out to do – that is, destroy the reapers.

    So in ME4, the wool that’s been put over our eyes concerning indoctrination is lifted, and Coats knows what he’s up against even better than Shepard did. He knows he can’t negotiate with these creatures, or overpower them, or even gather everyone together and destroy them with force. He can take a lot of paths and see a lot of different side missions, and meet characters that Shepard met and see how she affected them, but there’s only one ending – the destruction of the reapers, the unfortunate fall of all synthetic life, and the remnants of galactic civilization beginning to pick up the pieces. I guess this ending could be slightly colored by how Shepard dealt with the krogan and the quarians; if the galaxy’s greatest warriors and engineers (respectively) are teetering on the brink of extinction, then that would certainly affect the ending and alter the tone of Mass Effect 5.

    I think maybe one reason players hated the endings is because they thought they were going to have more of an effect on the outcome (like in Dragon Age: Origins). And while I understand this charge, there’s also the fact that 1) the Shepard’s mission was to destroy the reapers, and how she dealt with Conrad Verner would probably have little weight on this outcome, and 2) Shepard’s choices did continually affect the gameplay until the indoctrination sequence in the rubble of London. We got chances to execute Lana Thanoptis in the first two games and a chance to learn about her rampage in the third game; now, do we really need to see how Shepard affected her during the ending battle cinematic?

    Also, here’s another idea I was toying with, but I never put it in the outline because I figured it was already too long as-is. The players could find a community of people who revere Shepard and act as a sort of underground railroad for anyone who wants to flee from indoctrinated societies. There, the player could see all kinds of characters whose lives were changed by Shepard. Of course, the leader of the community would have to be none other than… wait for it… here comes a plot twist… DOCTOR CONRAD VERNER. He would still have to be a moron, but we could at least see him growing up morally. At this point he knows the difference between right and wrong – and he just so happens to be surrounded by competent people who can help him get things done. And if he’s dead, it could be some other bumbling moron hopelessly in love with the legendary Shepard.


  4. Pingback: Mass Effect: Planet of the Reapers! | kylebstiff

  5. BioWare and EA’s upcoming game in the acclaimed Mass Effect series should have been called Mass Effect 4, but the fact that the new title’s

    predicted numeric attachment was changed to one that plainly speaks about a famous galaxy says a lot about what we can expect, and also about

    what we may not. I am expecting a lot of things from this game. Let’s just wait for it to release now.


    • Hello John Smith!

      I used to be pretty miffed that BioWare painted themselves into a corner by painting themselves out of the traditional Mass Effect setting (can’t set a game within three wildly divergent settings as seen at the end of ME3), but now I’m looking forward to it. I’m glad they’ve set up shop in a new area. There’s no telling where the writers will be led by the vast, invisible macrobes that guide their hand!


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