Anderson in Mass Effect 3

Mass Effect trilogy plot summary


Mass Effect was a landmark video game trilogy released from 2007 to 2012. It included multiple ties-in such as novels, comics and an animated movie. Further games will follow in 2016 and beyond, although they will form a separate storyline.

It is a science fiction story, of the starships and space aliens kind. Most of the action takes place in a military context, as an apocalyptic threat against the galaxy emerges. It’s one of my favouritest games ever. offers extensive Mass Effect coverage. The core articles are setting for Mass Effect 1 and the setting for Mass Effect 2, plus the profiles for the heroine – Staff Commander Mandala Shepard.


This is a general, non-technical article that sums up the overarching plot of the 3 Mass Effect games plus DLCs and comics. It is intended as reference material so our Mass Effect character profiles and setting articles do not have to repeatedly explain the same things.

Needless to say, it is a gigantic S P O I L E R. And being spoiled would be a shame, since the trilogy is one of the very best computer games of the 2000s and piecing together what is going on requires some investigative effort.

This article doesn’t cover the events in Mass Effect 3 itself, but includes all the relevant data from the Leviathan DLC, the final version of the Extended Cut, and the From Ashes DLC.

Machines of loving grace

More than a billion years ago, colossal maritime creatures called the Leviathans  became the dominant species of the galaxy – as they refined a psychic influence power that could put entire planets under their thrall. The seemingly immortal Leviathans gradually imposed themselves as gods, with innumerable aliens races giving them tribute.

However, the Leviathans noted that they consistently lost thrall species as these developed synthetic life — self-aware robots — that turned against their creators. This pattern had also existed before the rise of the Leviathans, and the immense creatures decided that this was the key problem with organic life.

They built an AI to roam the galaxy and find a solution, by analysing all data about the development of organic and synthetic life. In their hubris, the Leviathans assumed that the machine they had created would never turn against them since they were so far superior to other organic life that they couldn’t possibly make mistakes.


However, the programming of the AI was actually terrible. Synthetic life always rebelling against organic life was given as axiomatic, and the AI’s goal to “preserve organic life” was ill-defined.

Given these parameters, the AI reached the conclusion that organic species should be stopped and archived/preserved before they developed sufficiently advanced synthetic life – for their own good. Based on the AI’s computations, 50,000 years after the development of complex tools was generally a good date to stop and archive organics before it was too late.

As the Leviathans axiomatically defined themselves as an “apex race”, the AI paid special attention to species capable of dominating all others – for instance through military conquest of large swathes of the galaxy. These were the ones that needed to be preserved.

And thus did the AI turn against the Leviathans, the “apex race” of that time. Though the organics vs. synthetics paradigm was erroneous, the Leviathans’ programming had made it a self-fulfilling prophecy.

Practically all Leviathans were exterminated, and their harvested genetic material was used to create a techno-organic version of a Leviathan – the first Reaper, named Harbinger .

The cycle

The galaxy-wide 50,000 years cycle of mass extinction was thus born. The “apex race” of each cycle would be harvested at the sweet spot of their development. Their collective genetic material would be used to create a new Reaper capital ship, inside which would be stored all information that the AI deemed important about their history, cultures, achievements, etc.

Commander Shepard meets the Leviathans under the sea

Three Leviathans.

The simplest hypothesis is that only the species deemed to be dominant is harvested, and everybody else is simply exterminated. Whether this is the case, or it is possible for several species to be harvested at the conclusion of a cycle — thus creating several capital ships — is unknown.

Though all Reaper capital ships outwardly resemble Leviathans, inside each shell is a sort of giant resembling a techno-organic version of the species harvested to create it.

With its growing horde of Reapers, the AI gradually made the 50,000 years cycle more efficient by having it follow a rigid script.

Pattern of the extermination

The mass relays and the Citadel  were created to impose this script on every cycle. The first species of a cycle to achieve widespread space travel would encounter mass relays, puzzle these out, then reach the Citadel – a perfect place from which to command and dominate the galaxy.

When the time for “preservation” came, the Reapers would come from nowhere and take control of the Citadel, then take control of the mass relays.

The spacefaring species would thus suddenly find themselves without their leaders and core governmental infrastructures. They’d also be stuck in disparate systems as the mass relays were closed, and probably deprived of their means of inter-clusters  communication.

The Reapers would then move en masse from system to system over centuries of methodical extermination. They would eliminate nearly all traces of these civilisations throughout the Milky Way galaxy.

The Normandy and the Destiny Ascension in front of the Citadel

The Citadel (front – the Normandy SR1 ; back – the Destiny Ascension).

The scenario was refined. The bulk of the Reapers would sleep in dark space (outside the galaxy) to conserve energy between extermination cycles. One Reaper capital ship would remain active and monitor the rise of the “apex race” and it reaching the Citadel.

This sentinel would only reveal itself at the conclusion of a cycle. It would the Citadel, lock out the mass relays from there, and summon the rest of the Reapers host from dark space. Reaper capital ships being immensely powerful and nigh-indestructible, one was sufficient for such a surprise attack.

The Reaper sentinel would also, during some cycles, arrange for a war between synthetics and organics if that didn’t occur naturally. This was was seen as axiomatically inevitable anyway.

This weakened possible opposition against the Reapers, since the AI didn’t want to lose a single Reaper. Each Reaper capital ship “archiving” an “apex race” the AI was to preserve forever against the threat of extinction by synthetics.

Still, at least 2 Reaper capital ships were killed before our cycle.

Stand amidst the ashes of trillions

Faced with the same scenario, successive organic civilisations generally developed similar responses – since none of them could hope to win against the immensely powerful Reapers.

However, all these responses ran afoul of the Reapers’ greatest weapon – indoctrination, their version of the psychic domination power of the Leviathans. Any sizeable project — for instance to weather the storm by entering suspended animation in hidden bases — would statistically involve at least one person secretly dominated by the Reapers, who could call a strike against the project.

Between the overwhelming might of the Reapers themselves and these omnipresent traitors, plus the technology to turn conquered organics into undead war machines, complete elimination was possible in nearly 100% of cases.

The extermination was so thorough as to remove most traces of intelligent life having been around. However on a galactic scale even a near-perfect clean-up left ruins and hints behind.

One rare exception was a species called the Rachni . Though the Reapers could easily indoctrinate the Rachni, they never managed to actually exterminate this insect-like species. How many cycles the Rachni survived isn’t precisely known, though, and they came very close to extinction during the modern cycle.

A Rachni queen

A Rachni queen.

Many species attempted to pass information to the next cycle. Though they were being killed off, they hoped to forewarn the civilisations of the next cycle.

That generally didn’t work. Furthermore the 50,000 years cycle was not long enough to really put that information to use, as developing technology capable of harming Reapers usually took much longer than that.

However, one specific design for a super-weapon kept being passed from cycle to cycle – albeit presumably not every, or even most, cycle. Those species who found it refined it and commented on it, gradually making it quite impressive.

The AI apparently decided not to expand resources to get rid of this. They knew that actually using such a super-weapon required plugging it into the mass relay network, which required controlling the Citadel, which was impossible once the end of a cycle had begun.

The last 100,000 years

The Prothean cycle

Several things went wrong during the Protheans -dominated cycle – the one preceding our own. What happened and why is unclear.

Unusual chronology ?

It is possible that the Protheans discovered Mass Effect technology unusually early, by investigating the wreckage left behind by the Inusannon – the dominant species of the previous cycle.

It is also possible that the synthetics vs. organics fight happened unusually early. This led the Protheans to forcibly unify all organics in the galaxy as it was necessary to win the war. This conflict was called the Metacon War, and might have raged for tens of thousands of years.

Unusual preparations for the next cycle ?

After the Reapers invaded, Prothean scientists studied primitive species at the cavemen stage, to determine which would be the dominant species of the next cycle.

They did not uplift  their subjects, so they would be ignored by the Reapers as being too primitive. Instead, they carefully planted resources to accelerate their development once the Reapers were gone. Genetic manipulation might also have been involved.

The most promising primitives were apparently the very early Asari, who thought that the Protheans were gods. The Protheans built and hid a knowledge archive right on Thessia, the Asari homeworld. The more common case was apparently Humanity’s – the Protheans also left us a secret knowledge archive, but it was on Mars.

The Protheans’ goal was to enter suspended animation, then emerge once the Reapers were gone, take charge of the primitives and build a new Prothean Empire capable of killing Reapers. The secret archives also contained the best and latest design of the Reaper-killing super-weapon, as inherited and refined over previous cycles.

This design was now nearly complete. In fact, the last surviving Protheans had started building it and testing it. However they ran out of time and resources, and discovered that they would have needed to access the Citadel for the weapon to be effective.

Highly improbable circumstances on the planet Ilos

One Prothean secret scientific facility, on the planet Ilos , was completely missed by the Reapers through a freak happenstance.

The scientists there went into suspended animation. After decades or centuries these facilities started running out of power – and the eradication of the Prothean Empire was still ongoing. The computer monitoring them eventually opted to wake up the last hibernating researchers, since it became clear the power reserves were insufficient to wait out the entire extinction.

Still, by this point, Ilos was far behind the extermination front, in a part of the galaxy that was assumed to be sanitised.

Prothean ruins on Ilos

Prothean suspended animation pods on Ilos.

The desperate scientists broadcast a message relayed by the Prothean communication beacons, but nearly all beacons in the network had been destroyed or lost.

Since no surviving Prothean would have been able to reach Ilos anyway, it seems likely that the message wasn’t addressed to the present but to the future. Perhaps they hoped that the Reapers had missed some beacons, and that the civilisations of the next cycle would discover such a beacon and its message.

(As hypothesised in our 6th entry for Commander Mandala Shepard, the message may actually have been a weapon – but though this hypothesis is oddly coherent is has no concrete support in the game.)

As everything was lost, the Prothean scientists on Ilos secretly built a sort of mini-mass relay compatible with the mass relay network. They used it to jump to the Citadel. At that point the Citadel had been abandoned by the Reapers, while a slave species of theirs called the Keepers  toiled to refurbish it for the next cycle.

The scientists subtly hacked the Keepers so they wouldn’t carry out certain orders when the next cycle would end.

The hidden archives somehow survive

The Reapers destroyed almost every Prothean suspended animation pod outside of Ilos, largely thanks to indoctrinated Protheans.

However, they did not realise what had happened on Ilos and the Citadel. Furthermore the archives left by the Protheans to promising primitives weren’t destroyed.

Hypotheses as to why the Protheans archive were not found include:

  • Extreme security measures such as deleting all records and having everyone kill themselves to remove all traces.
  • The unique data storage medium used by Protheans — who have seemingly unprecedented senses in galactic history — eluding Reapers sensors.
  • The Reapers considering that the Archives wouldn’t help much and choosing not to expend energy to destroy them.

No Prothean-based Reaper capital ship ?

It was apparently impossible to create a Reaper capital ship from Prothean DNA. One gets the impression that something about Protheans did not work in the same way as with previous organic species (or at least previous “apex races”).

Creation of the Collectors

Thought a Prothean Reaper seemingly couldn’t be created, the massacred Protheans were turned into undead-like creature called Collectors. These could “live” for tens of thousands of years and were used as agents by the Reaper monitoring the galaxy.

The Collectors were presumably the closest approximation of “preserving” the Protheans. In actuality, it was but a horrible and lifeless mockery of whom the Protheans had been. Even these husks gradually degraded, though, and organs were increasingly replaced by cybernetics to keep them running.

The modern cycle

In large part due to the efforts of the dying Protheans, the next cycle started off-script – and that became even worse 50,000 years later.

New Asari (dis)Order

The rise of the Asari was accelerated by Protheans protection (for instance, they shielded Thessia from a meteor impact that would have triggered an ELE) and the Thessia knowledge archive. The Asari thus became the species that discovered the Citadel.

However, with no Prothean to emerge from suspended animation to conquer them, the Asari were left to do things their way.

While they have a generally chaotic nature, the Asari are no conquerors. They developed societies based on alliances, exogamy and individualism. They did not use the Citadel to impose their rule and/or culture on other species, but to run politics and create alliances with the most powerful species as they emerged on the galactic scene.

In time they let a successful species, the Salarians, co-manage Citadel Space with them.

Peace and prosperity

Thus, this cycle was relatively free of pangalactic wars weakening everyone – though it can also be argued that it resulted in slower developments for military technologies.

The Reaper capital ship watching the galaxy, Sovereign , apparently grew concerned about this. It found and indoctrinated several Rachni queens, having them and their offspring attack other organics.

That one was a close call and was only survived thanks to the Salarians uplifting the Krogans. However the situation with the Krogans eventually became as bad as the situation with the Rachni — until the Asari and Salarian recruited and bolstered the Turians to fight the Krogans.

This was another close call, but the Krogans were defeated. The Asari let the Turian Hierarchy co-manage Citadel Space with them and the Salarians – since Turians were much better frontline soldiers than either the Asari or the Salarians.

Portrait of Liara T'Soni in ME2

One fine Asari specimen.

Artificial Intelligences banned

One gets the impression that the Asari had rules against AIs and synthetic life from the get-go. If so, one assumes that it was something they learned from the Protheans in their prehistoric myths, and later on from the Prothean Archive on Thessia.

There were of course numerous small-scale illegal attempts to develop AIs, but doing it on the scale usually practiced during previous cycles wasn’t possible.

Thus, an entire species of synthetics only happened a mere 300 years before the end of the cycle, when the Quarians accidentally created the geth.

They may be synthetics but they’re not stupid

The Reaper sentinel, Sovereign, approached the geth to put things back on-track and have them turn against the organics. Howbeit, only a minority of geth followed him, apparently due to a freak CPU bug.

Furthermore, most geth weren’t interested in attacking organics. This was seemingly a result of political events on the Quarian homeworld when the geth “awoke”. A movement of Quarian activists had done what they could to hide and protect the geth, considering that they were living beings and hadn’t done anything wrong.

Thanks to their sacrifice, the geth reached the conclusion that they needed to understand organics better, rather than deciding that organics were axiomatically a threat.

Things man was not meant to know

Some years before the end of the cycle, eccentric Human researchers assembled clues that hinted at the existence of a handful of Leviathans – who had been hiding for more than a billion years.

Enters the dragon

Mass Effect

A few years before the end of the cycle, Sovereign indoctrinated an agent of the Asari/Salarian/Turian Citadel Council. This Turian, Saren Arterius , did piece together what the Ilos plot had been 50,000 years before. He then worked to find more clues as to its exact nature — and undo whatever the Prothean scientists had achieved.

Arterius would have been successful, as he eventually found the Ilos base and the mini-mass relay there. He also could draw endless troops from those geth who had agreed to serve Sovereign.

However, Saren ran into a Human, Staff Commander Shepard. Against all odds, the Commander kept pursuing Saren. With the help of an Asari archaeologist named Dr. Liara T’Soni, reconstituted what had been the Prothean plot on Ilos almost as fast as Saren did.

The Commander was also accidentally exposed to what may have been the last Prothean beacon holding the Ilos message. Using this information T’Soni gained some insight into the coming of the Reapers, and she and Shepard obtained enough information to understand the rough workings of the galactic extinction cycles.

Commander Shepard calmly peers through the smoke

Staff Commander Mandala Shepard.

Still, Saren was about to reduce the efforts of the Ilos Protheans to naught mere hours before the end of the cycle.

As Sovereign and his enthralled geth were attacking the Citadel as per normal procedure, Saren finished investigating Ilos. He then used the Protheans’ own miniature mass relay to jump to the Citadel. Though the Keepers were unresponsive to Sovereign’s orders, Saren could still reach the secret controls the Keepers were meant to operate and do the job in their stead.

Shepard came in in hot pursuit. She confronted Saren right as the Turian closed the Citadel around Sovereign – so Sovereign could take full control of the Citadel undisturbed. The Commander killed Saren and switched the Citadel back into open position, unexpectedly exposing Sovereign to the defenders’ naval artillery.

Sovereign expended a huge amount of energy to remotely reanimate Saren’s corpse and use it to close the Citadel. Nevertheless, the Commander and her unit killed the revenant. The Reaper capital ship, its shields weakened by the massive energy expenditure, was then killed by Fleet-level, massed naval fire.

These are the events in the first Mass Effect game.

Mass Effect 2 and Mass Effect: Redemption

In dark space, the Reaper armada awoke to discover that one person had completely messed up the script and was responsible for the death of Sovereign.

The first and mightiest Reaper, Harbinger, then took control of the Collectors. These were tasked with murdering Commander Shepard, then start harvesting Humans – though on a much smaller scale than what the Reaper capital ships could do.

Shepard’s exploits had apparently led Harbinger to the conclusion that the Humans, not the Asari, were the apex species of this cycle. The rapid growth of Human military power may also have played an important role.

Commander Shepard and Doctor T’Soni attempted to convince the Citadel Council  and their respective governments of the existence of the Reapers and the extinction cycle. However, they lacked proof and ran afoul of the conservatism and preference for secrecy of these bodies, who suppressed the information.

The Collectors did kill the Commander in a surprise attack. Harbinger ordered her corpse taken and examined to determine how she had defeated Sovereign, but *this* plan was defeated by Dr. Liara T’Soni and, impossibly, Shepard was back 2 years later.

The full squad roster in Mass Effect 2

Shepard’s tactical squad in Mass Effect 2.

Shepard waged war against the Collectors to stop their attacks against isolated Human colonies. Impossibly enough, she managed to defeat them then destroy their base as well as the Human-based Reaper they had been growing/building.

By this stage both Harbinger and the surviving Leviathans considered that Commander Shepard was an anomaly threatening the entire cycle mechanism.

Shepard then discovered which mass relay would let the Reapers enter the galaxy and blew it up against impossible odds, delaying the end of the cycle by 6½ months.

These are the events in Mass Effect 2 (including the DLCs) and the Mass Effect: Redemption comic book.

When the Reapers do reach the Milky Way galaxy they go straight for Earth, but Commander Shepard escapes.

The Reapers do not attempt to take the Citadel. Apparently, it is no longer possible to use the Citadel to shut down the mass relay network – one assumes that this is simply a consequence of the hidden room with the controls having been destroyed during the killing of Sovereign.

This is when Mass Effect 3 starts.

By Sébastien Andrivet.

Source of Character: Mass Effect video game trilogy.

Writeup completed on the 28 of July, 2013.