Spoiler note: Mass Effect 3's story is divided into three acts and doles out major moral choices at the conclusion of each. This article discusses these choices in detail, although is written so it can be read in sections. The article's first section discusses the choices made up to and including the mission on the krogan homeworld of Tuchanka. The article's second section details those found at the end of the second act, concerning the quarian-geth war. The final section discusses the game's ending.
Mass Effect is a series shaped by the player's design. From the gender and sexual orientation of its lead character to the fates of key players and entire races, the series has never shied away from big decisions. Mass Effect 1 forced players to sacrifice one squad member over another on the planet Virmire, decide whether to eliminate the Rachni race for good, and choose whether to execute or save party member Wrex. The conclusion of Mass Effect 2 broadened the story's sprawling options further, allowing any or all of the main characters to die, from a party as large as 12.
Mass Effect 3 has the unenviable job of continuing that story, its plot having to wriggle and wrap its way around the universe you have created. Those new to the series will find certain decisions have been made for them - your Shepard will have destroyed the Collectors' base at the conclusion of Mass Effect 2, for example, while players present at the last game's finale had the choice of handing it over to the morally grey Cerberus.
Act One: Tuchanka and the genophage cure
The first act's conclusion revolves around the reversal of the genophage, a weapon that has drastically reduced the war-like krogan race's fertility. Its removal is necessary to win their support in the ongoing galactic war. Shepard is presented with a choice: either to facilitate the dispersal of a cure, or secretly sabotage it. Pursuing the latter option will enrage the krogans but please the genophage-creating salarians, ensuring their backing instead.
Your Shepard's stance on the situation will likely cost the lives of one of two major characters, krogan leader Wrex or Mordin, your salarian Mass Effect 2 squadmate who was instrumental in the genophage's development.
Mordin is a complex character and embodies one of the series' best morally grey plotlines. The genophage helped end a costly war between the krogan and other races, saving countless lives at the cost of a species now left without hope of flourishing again in the future. The previous game saw Mordin begin to regret his work after meeting an old student of his, Maelon, performing horrific experiments in an attempt to find a cure. Shepard shut down Maelon's lab due to its butchery, but could choose whether to destroy or save the valuable research data it had gained. Thus, in Mass Effect 3, choosing to help Mordin finally cure the genophage and secure krogan support can be seen as morally the best option to take. But doing so will result in Mordin's death, as he sacrifices himself to deploy the cure amongst Reaper bombardment.
Shepard can inform Mordin and Wrex (or the surlier Wreav, his replacement if you killed Wrex in Mass Effect 1) of the salarian leader's sabotage plot, ensuring the cure is successfully deployed. Alternatively, Shepard can conceal the plot, although Mordin will eventually deduce what's going on. Here, Shepard can allow Mordin to deploy the cure anyway, although he parts with Shepard on furious terms. Or, Shepard can choose to shoot Mordin, violently stopping him from deploying the cure in a heartbreaking scene. This will mean the krogans are tricked into providing their support, although Wrex will later discover your deception and you will be forced into a confrontation where Wrex will die.
Then there's the third option. If your Shepard has been seriously opposed to the krogans and the possibility of them ever recovering from the genophage, you can force an option where Mordin stands down. No cure is released, and Mordin lives. But this is only possible if you executed Wrex in Mass Effect and either destroyed Maelon's data in Mass Effect 2 or failed to complete a previous mission in Mass Effect 3 defusing a nearby bomb. Either of these last two options will result in the loss of Eve, the krogan female Mordin has been helping. Without both Wrex and Eve, portrayed as the stabilising future leaders of the krogan race, Mordin will agree it is best that the krogans are not granted their freedom just yet.
Which is best? One results in the death of Mordin and the gain of krogan support, the other the death of Wrex and the gain of salarian support. The third appears the best on paper, but is the least satisfying in terms of story. Throughout the mission you travel through the ruins of ancient krogan civilisations, founded before the race discovered nuclear weapons, and, armed, flew into space. For the first time, you uncover a small grassy area of the world attempting to flourish anew. The metaphor couldn't be clearer.
Act Two: The quarians and the geth
The second act deals with the geth, a synthetic race who achieved sentience and eventually rebelled against their creators, the quarians. The geth eventually seized control of their homeworld and left the quarians as migrants, living on an armada of ships constantly seeking resources, shunned by the galactic neighbourhoods they turn up in.
The act's denouement sees the quarians attempt to reclaim their homeworld. The geth have reluctantly accepted aid from the Reapers to ensure their survival and Shepard's mission to destroy the Reaper presence will make them vulnerable. The mission can end with the complete destruction of either race, or Shepard can try a third option to broker a peace.
With the Reaper base destroyed, Legion will try and sacrifice itself to upload a copy of the Reaper tech to his now vulnerable race, ensuring their defence against the attacking quarians. But doing so will cause the geth to wipe out the quarians altogether. Choosing to support Legion will cause Tali to commit suicide after seeing her entire species wiped out, with the consequence that she is lost as a party member.
Siding with Tali and the quarians meanwhile causes Legion to attack, and you are forced to kill "it" while the rest of the geth is wiped out via the quarian aerial bombardment.
To broker a ceasefire, Shepard must have a high reputation score and have completed the majority of a whole checklist of conditions. These include the preceding two missions helping the quarians and, in one of these, the choice to save an admiral at the cost of his crew. He will now back up Shepard when trying to barter the ceasefire. Long-time quarian squadmate Tali must have survived Mass Effect 2's ending. As must Legion, the friendly geth you salvaged who could become a party member, should you choose to activate him in the first place. Completing Tali's Mass Effect 2 loyalty mission is also important, as it saw her able to return from exile and become an admiral herself. Without importing a save, Mass Effect 3 assumes she is still an outsider.
Players still not able to unlock the dialogue options to prompt the ceasefire despite completing these options are still debating what other decisions affect the outcome, including the Mass Effect 2 decision to destroy or rewrite Reaper-aligned geth forces.
If successful in securing a ceasefire, both quarians and geth will join the war effort, doubling your support.
Act Three: Mass Effect 3's ending options
Previous decisions in the series did not have the luxury of completely changing Mass Effect's world for fear that the saga's branching storyline would become too disparate to control. Mass Effect 3's ending need not have that worry, being the last chapter from the universe for the forseeable future. But each of the game's endings conclude fairly similarly, barring a few variables.
Mass Effect 3 has three main ending options, each flavoured better or worse by your final Galactic Readiness score. All result in the same thing: the defeat of the Reapers and the galaxy saved, while the Normandy crash lands on an alien planet.
After battling to the Crucible (your handy Reaper killing machine) a Reaper intelligence briefs you on your three options (three actual, physical pathways), one of which you must slowly stumble down towards your destiny.
The first allows Shepard to control the Reapers. This is portrayed as the Renegade option, a choice represented by a vision of the Illusive Man, the game's major human antagonist. Choosing it melds Shepard's conscience with the Reapers, annihilating his physical form but calling them off. The power of the Reapers is still a factor, and it is repeatedly stated that such a power should not be controlled by one man.
The second option is to destroy the Reapers. This is portrayed as the moral "Paragon" option, represented by a vision of Captain Anderson who the Illusive Man has just killed, *sniff*. Choosing it will blast the Reapers out of the sky but will also destroy all other AI, including the geth and your ship's newly conscious computer EDI.
Throughout the game EDI's path to self-awareness has been a major plot-point, while the Paragon path will also lend itself to players attempting to broker peace with the geth. Both will effectively be undone in this ending, but it is the only ending where Shepard has a chance of surviving - a two second clip of his body stirring amongst the rubble is shown if you have a significantly high enough Galactic Readiness rating.
Then there's the third option, sacrificing Shepard to merge his consciousness with the Reapers' technology and re-write the galaxy's DNA. It means there will be no more purely-organic or purely-synthetic life: everything will be a mix of the two, and will end the Reapers' cycle for good.
It is slightly depressing that this is seen as the 'best' option, only unlocked with a far higher Galactic Readiness than either of the two others. The message that the only way two sides of a war can survive by losing individuality is perhaps a downbeat one, suggesting there is no way that either side would ever truly achieve peace side by side.
So the Mass Effect trilogy ends, in a two-minute cut-scene where your choice is reflected in the colour of an energy wave erupting from the Crucible. The wave covers Earth and fires through the Mass Relay network across the rest of the galaxy.
The 'destroy' and 'merge' endings clearly show the Mass Relay network exploding, effectively ending the ability for fast galactic travel. These also show the Citadel exploding, presumably killing anyone left on board. A higher Galactic Readiness rating ensures the survival of those on Earth and your crew members, and is easier to achieve if you destroyed the Collector Base at the end of Mass Effect 2.
It is perhaps fitting that none of the game's endings conclude on a completely good or bad note. Mass Effect's story works best when the player is entrusted with questions to which there is neither an entirely right or wrong answer. But unlike the series' other moral quandaries, the ending offers little difference between its options. After sowing so many disparate story strands throughout its trilogy, BioWare must feel a duty to align the grand strokes of the Mass Effect universe for whatever lies next.