Mass Effect 1
Commander Shepard is made a Spectre and assigned to take down another Spectre gone rogue, Saren Arterius. As it turns out, Saren’s “ship” Sovereign is actually a Reaper, and Saren is working for it. Sovereign wants to summon the rest of the Reapers so they can wipe out all technologically advanced life, which is something the Reapers do once every 50,000 years. Shepard stops Saren and leaves Sovereign vulnerable, allowing the Citadel fleets to destroy it and save the day.
The Normandy SR-1 is assigned to a secret mission: to secure a Prothean beacon recently unearthed on the human colony world of Eden Prime. The planet falls under geth attack: Saren Arterius, a Spectre agent gone rogue, is working with the Reapers and with the “heretic” geth to obtain access to the beacon. Commander Shepard, Kaidan Alenko, and Richard Jenkins are ordered to land and take control of the situation. Jenkins is killed in action. The remaining two encounter Ashley Williams, who aids them in locating the beacon. Shepard uses the beacon, which imparts on their mind a vision (a distress call sent out in the final days of the Prothean empire). However, Saren had already used the beacon and fled.
The Normandy travels to the Citadel, where the Council is skeptical of their claim that Saren has gone rogue. Shepard and crew recruit Garrus Vakarian, Urdnot Wrex, and Tali’Zorah nar Rayya into the squad; Tali has evidence linking Saren to the geth, which the Council accepts as proof of Saren’s treason. Saren is stripped of his Spectre status, and Shepard is elevated to a Spectre and tasked with bringing Saren in to face justice. An important asari, Matriarch Benezia, is also implicated, and it is revealed that Saren’s plan is to locate the Conduit and bring back the Reapers.
The Normandy travels to Therum. Matriarch Benezia’s archaeologist daughter, Liara T’Soni, is discovered, saved from the geth, and recruited into the squad.
The Normandy travels to Feros. The crew fights off the geth that threaten the colony, then discovers that Feros harbors a unique life form, the Thorian. The Thorian is ancient enough that it once lived alongside the Protheans, and telepathic enough that it has memories of their experiences. However, the Thorian is hostile to Shepard and must be killed. Shiala, an asari acolyte of Matriarch Benezia, had telepathically melded with the Thorian to receive the “Cipher” (the experience of being a Prothean) and then share it with Saren (which was necessary to interpret the vision he received from the beacon on Eden Prime). Shiala, now released from thralldom under the Thorian, is grateful to Shepard and shares the Cipher with them.
The Normandy travels to Noveria. The crew discovers that Saren has been funding research into breeding rachni as soldiers, but the rachni got free and Matriarch Benezia was sent to contain the situation. They encounter Benezia, fight her, and kill her. Benezia reveals that she has been indoctrinated by Saren’s “ship” Sovereign (actually a Reaper). She also reveals that Saren needed the location of the Mu Relay, which she obtained telepathically from the mind of the rachni queen, but Benezia did not know why the Mu Relay was needed. Benezia then dies.
The Normandy travels to Virmire. A salarian STG unit has been pinned down while trying to collect intel on Saren’s base of operations. Saren has cured the krogan genophage and is breeding an army of krogan loyal to him. Shepard’s team and the salarians hatch a plan to infiltrate the base and set off a nuclear device inside it. Wrex is not happy with this plan; if Shepard cannot convince him, Wrex will be killed. Shepard encounters another Prothean beacon, this one having a complete version of the vision Shepard partially received on Eden Prime. Shepard discovers a console that connects to Sovereign, discovers that it is a Reaper, and has a conversation with it. Shepard and the salarians place the bomb, but Kaidan and Ashley become separated and each comes under geth attack; Shepard must choose which to rescue, and the other dies in the nuclear explosion.
[ME1: Bring Down the Sky DLC] The Normandy travels to asteroid X57 above Terra Nova. The asteroid was inserted into orbit around the planet with fusion torches, but batarian terrorists have hijacked the asteroid and plan to crash it into the planet. Shepard disables the fusion torches and fights his way to the terrorist leader, Balak. Balak has hostages. Shepard must choose whether to let Balak go to save the hostages, or to let the hostages die while fighting Balak to the death.
Now that Shepard has Liara’s Prothean expertise, the Cipher from Feros, and the uncorrupted version of the beacon vision from Virmire, they can piece together the fact that the Prothean artifact that Saren seeks is located on Ilos, a planet only accessible through the Mu Relay.
Armed with this knowledge, Shepard returns to the Citadel and requests that a fleet be sent to Ilos to stop Saren. The Council refuses, believing that Saren plans to attack the Citadel with conventional tactics and that the Conduit he seeks is irrelevant, and they forbid Shepard from taking the Normandy into the Terminus Systems where Ilos lies. Shepard steals the Normandy and goes there anyway.
On Ilos, Shepard and crew chase Saren. They are diverted when a force field blocks their path; initially suspecting a trap laid by Saren, they instead discover that a Prothean VI, Vigil, wishes to speak to them. Vigil tells them the history of how the Protheans were wiped out by the Reapers, and of how the Citadel is part of the Reaper trap. It also reveals that the Conduit Saren seeks is a miniature mass relay, a backdoor to the Citadel. Shepard and company use the Conduit to reach the Citadel, only minutes behind Saren.
On the Citadel, the team fights their way to Saren as a battle rages outside: the geth fleet clear the way for Sovereign to attach itself to the Citadel and activate it as a mass relay to dark space, and the ward arms close, sealing Sovereign safely away from the reach of the Citadel defense fleet. Shepard finds and defeats Saren, then uses a data disk given by Vigil to regain limited control of the Citadel. They open the ward arms and Shepard decides whether to order the human fleets to rescue the Citadel defense fleet (including the Citadel Council) or to focus fire on Sovereign. In either case, the human fleet destroys Sovereign, and the day is saved.
If the Council survived, they reward humanity with a seat on the Council for their bravery, and lingering hostilities toward humanity are reduced. If the Council died, humanity takes control of the galaxy, appointing a new Council which is either human-led (Anderson made councilor) or all-human (Udina made councilor), and those lingering hostilities are fanned.
- Recruit Garrus, Wrex, or both
- Spare or kill the enthralled colonists on Feros
- Talk down or kill Ethan Jeong on Feros
- Spare or kill Shiala on Feros
- Spare or kill the rachni queen on Noveria
- Talk down or kill Wrex on Virmire
- Assist salarian Capt. Kirrahe or not on Virmire
- Save Kaidan or Ashley on Virmire
- [ME1: Bring Down the Sky DLC] Let Balak go or kill him
- Save the Council or hold back the fleets at the final battle
- Recommend David Anderson or Donnell Udina for position of Human Councilor after the final battle
Mass Effect 2
Commander Shepard dies, but the human-supremacist organization Cerberus uses science to resurrect Shepard. The Collectors are abducting human colonists in secret, and Cerberus wants Shepard to find out why and stop them. Shepard builds a team, discovers that the Collectors are working for the Reapers, and obtains a means of reaching the Collector Base. Shepard and team go on a suicide mission to the Base, and they discover that the Collectors are building a new Reaper from the kidnapped human colonists. Shepard either destroys the Collector Base or captures it for Cerberus to use. In either case, the partially-completed Reaper is destroyed.
The Normandy SR-1 has been assigned to wipe out pockets of geth resistance after the events of ME1. The SR-1 is discovered by a Collector ship, attacked, and destroyed. Most of the crew reach the life pods, but Shepard is killed while saving Joker.
Two years pass. Shepard is resurrected by the pro-human terrorist organization, Cerberus, and meets the Illusive Man holographically. Human colonies are being abducted wholesale, and the Alliance is sweeping things under the rug. Shepard reluctantly agrees to work with Cerberus to investigate.
Shepard and two Cerberus operatives (Miranda Lawson and Jacob Taylor) travel to Freedom’s Progress, a human colony which just had its colonists abducted. There he finds a traumatized quarian eyewitness, Veetor’Nara, who has video evidence pinning the abduction on the Collectors. Shepard decides to use the resources Cerberus is giving them to stop the Collectors. The Illusive Man reveals that Joker has joined Cerberus, and Joker reveals that Cerberus has constructed the Normandy SR-2.
[ME2: Kasumi: Stolen Memory DLC] Shepard goes to the Citadel and recruits Kasumi Goto with no trouble.
[ME2: Zaeed: The Price of Revenge DLC] Shepard goes to Omega and recruits Zaeed Massani with no trouble.
Shepard goes to Omega to recruit Mordin Solus. Along the way, Shepard helps Mordin cure a multi-species plague which was likely engineered by the Collectors.
Shepard goes to Omega to recruit “Archangel”, a vigilante who turns out to be Garrus. Shepard helps Garrus decapitate the Blue Suns, Eclipse, and Blood Pack mercenary gangs on Omega.
Shepard goes to the prison ship Purgatory to recruit Jack. The warden decides to kidnap and ransom Shepard. Shepard releases Jack, kills the warden, and escapes.
Shepard goes to the shipyard planet Korlus to recruit Warlord Okeer. Okeer dies, but he has been attempting to use genetic science to construct the “perfect” krogan. If Shepard chooses to decant this “perfect” krogan out of his tank, Shepard names the krogran Grunt and recruits him.
Shepard goes to the human colony world Horizon, where the Virmire Survivor (Kaidan or Ashley) was stationed to identify the culprit. Shepard discovers evidence that the Collectors are working for the Reapers, proving a hunch of the Illusive Man. Shepard meets the VS, but it doesn’t go well, as the VS is upset at Shepard for working with terrorists.
Shepard goes to the planet Illium to recruit Thane Krios. Thane is on a mission to assassinate Nassana Dantius, a corrupt businesswoman. Shepard inadvertently assists Thane, and Thane joins Shepard.
Shepard goes to the planet Illium to recruit Samara. Samara is on a mission to locate an Ardat-Yakshi, her own daughter Morinth, and kill her. However, a local police officer has been ordered to detain Samara. Shepard succeeds in tracking down the name of the ship in which Morinth escaped, earning Samara’s gratitude. Samara chooses to swear the Third Oath of Subsumation, pledging allegiance to Shepard for the duration of the Collector mission.
Shepard goes to the abandoned quarian world Haestrom to recruit Tali’Zorah. Tali is on a mission to collect readings on Haestrom’s sun, which is behaving strangely. However, Tali was pinned down by geth and the squad of quarian marines protecting her has been eliminated. Shepard rescues Tali, and she joins the team.
Shepard boards a powered-down Collector vessel which was apparently disabled by a turian patrol. This proves to be a trap, but EDI successfully scans the vessel’s computers to determine how to reach the Collector Base. They successfully escape the vessel and return to the Normandy before the vessel can power up weapons.
Shepard assists Miranda on Illium with relocating her sister. She and her sister Oriana escaped from their father, Henry Lawson, who is a powerful businessman and a control freak, and Miranda discovers that her father has located the safe house where she hid her sister’s adoptive family. However, her trusted friend, Niket, plans to return Miranda’s sister to the elder Lawson, because he discovered that Miranda’s sister was not old enough to consent to leaving, making Miranda’s escape from their father a kidnapping. Niket is killed by the very mercenaries hired by the elder Lawson, and Shepard and Miranda stop the mercs.
Shepard assists Jacob on 2175 Aeia with investigating his father’s sudden reappearance. Jacob’s father was on a ship that crashed on the unexplored world, and the distress beacon was finally activated 10 years later. They land and discover a situation straight out of Joseph Conrad’s “Heart of Darkness”, with Jacob’s father as the corrupt ruler over a populace that lost their intellect to a poison in the native plant life.
Shepard assists Mordin on Tuchanka with “rescuing” Maelon, a former protégé who has been “kidnapped”. It turns out that Maelon is using unethical experiments to cure the genophage (in a misguided attempt to assuage his guilt at participating in the genophage renewal project), and Clan Weyrloc (an enemy of Clan Urdnot) stands to reap the benefits. Shepard possibly talks Mordin out of killing Maelon, and possibly preserves Maelon’s data in hope of a future cure under more ethical circumstances.
Shepard assists Grunt on Tuchanka with a coming-of-age ritual, the Rite of Passage. The team must fight ferocious animals to tame Grunt’s pubescent blood haze instinct. Grunt earns membership in Clan Urdnot.
Shepard assists Jack on Pragia with destroying her childhood prison.
Shepard assists Garrus on the Citadel with tracking down Sidonis, a man who betrayed Garrus in cowardice by bringing about the deaths of Garrus’s vigilante squadmates to save his own life. Shepard possibly talks Garrus out of sniping Sidonis.
Shepard assists Thane on the Citadel with setting Thane’s son, Kolyat, on a better path. Kolyat has decided to follow in his father’s footsteps as an assassin, a path which Thane does not want him to walk.
Shepard assists Samara on Omega with tracking down Morinth for good. Shepard may choose to betray Samara in favor of Morinth, but one or the other must die.
Shepard assists Tali within the Migrant Fleet by standing as her captain at her trial for treason: she is accused of shipping live geth parts back to the fleet, resulting in the loss of the lab ship Alarei. When Tali gets the opportunity to exonerate herself by reclaiming the Alarei from the geth, Shepard agrees to help. Depending on Shepard’s dialogue choices and persuasiveness, Shepard can get Tali cleared of all charges, get Tali exiled, or lose her trust by revealing the truth of the Alarei (her own father was conducting illegal experiments on live geth).
[ME2: Kasumi: Stolen Memory DLC] Shepard assists Kasumi on the human colony world Bekenstein with stealing the graybox of Keiji Okuda, her dead lover, from Donovan Hock, the man who killed Keiji. They seemingly succeed at the heist, but must fight their way out of Hock’s mansion.
[ME2: Zaeed: The Price of Revenge DLC] Shepard assists Zaeed on Zorya, a human resource world, with liberating an energy refinery held by the Blue Suns mercenaries. They encounter Vido Santiago, the leader of the Blue Suns and the man who betrayed Zaeed. Zaeed acts recklessly, endangering the very refinery they were sent to liberate. Shepard chooses either to pursue Vido, leaving the refinery workers to die, or to save the workers, giving Vido time to escape in a gunship. If Vido escapes, a very persuasive Shepard can talk Zaeed into remaining loyal.
Shepard boards a long-dead Reaper floating derelict in space, with the assignment of obtaining the Reaper’s IFF. A Cerberus science team aboard the Reaper became indoctrinated and husk-ified, and Shepard must fight through them. Shepard encounters a lone geth sniper which assists Shepard, to the team’s disbelief. This geth platform, containing non-heretic “true” geth, is attacked by husks and disabled, so Shepard and team carry it back to the Normandy for observation and study. Shepard optionally chooses to activate the platform, naming the geth “Legion” and recruiting them.
Shepard assists Legion in preventing the “heretic” geth from rewriting the “true” geth with a virus. Shepard may choose to destroy the heretics or to forcibly rewrite them into “true” geth.
The Normandy crew has installed the Reaper IFF, but it is behaving unusually. Shepard and all squad members leave aboard the shuttle. The IFF is actually transmitting the SR-2’s location, which attracts the Collector ship. The Collectors board and kidnap all of the crew except Joker. Joker successfully unshackles EDI, allowing her to purge the ship of Collectors by opening the airlocks and jumping to FTL.
Shepard and the squad members return to the SR-2. With the crew kidnapped, the urgency grows for taking the fight to the Collectors.
Shepard makes the choice to use the Omega-4 relay, starting the Suicide Mission. As Shepard and his squad infiltrate the Collector Base, they attempt to rescue the crew and then attempt to destroy the base. Shepard makes a series of choices that massively influence the number of people who die: from squad and crew 100% alive, to everyone but Joker dead (even Shepard). At the end, Shepard must choose whether to destroy the base entirely, or whether to just set off a radiation pulse that will kill the Collectors but leave the base intact for the Illusive Man and Cerberus to get their hands on.
[ME2: Overlord DLC] Shepard goes to a Cerberus facility on Aite. As Shepard works to contain the situation, they learn that Dr. Gavin Archer was attempting to control the geth by interfacing a human mind with a VI to create a hybrid intelligence. It is revealed that he forced his autistic savant brother, David Archer, to be the human mind in the experiment. The experience was painful and confusing, causing David to lash out in an attempt to silence the noise in his head. Shepard either allows Dr. Archer to continue the experiments, or else sends David Archer to Grissom Academy where they can help David recover and live a reasonably happy life.
[ME2: Lair of the Shadow Broker DLC] Shepard goes to Illium and gives Liara information about the location of her friend Feron, who was imprisoned by the Shadow Broker. Shepard heads to Liara’s apartment to meet her, but someone has attempted to assassinate her. Shepard works with a fellow Spectre agent, Tela Vasir, to locate Liara, but unknown to Shepard, Vasir is working with the Shadow Broker. The Shadow Broker bombs the building where Liara fled, and Vasir steals the data on where the Shadow Broker is hiding. Shepard and Liara chase Vasir and kill her, retrieving the data, then assault the Shadow Broker’s secret base. They kill him and rescue Feron. With the Shadow Broker dead, Liara takes control of his organization, becoming the new Shadow Broker.
[ME2: Arrival DLC] Shepard breaks into a batarian prison in the Bahak system to rescue Dr. Amanda Kenson, a friend of Admiral Hackett. Kenson tells Shepard that the Reapers will be invading the galaxy in a matter of days, arriving in the Bahak system and using the unusually powerful mass relay there to invade the galaxy in one strike. Kenson and her team were planning to destroy the relay with an asteroid impact, which would wipe out the entire Bahak system, but were torn by the resulting loss of life. Shepard demands proof, and Kenson presents Object Rho, an unshielded Reaper artifact which shows Shepard a vision. Kenson and her team were indoctrinated by the artifact, and they capture Shepard. Shepard must fight their way out of confinement, destroy the relay, and escape at the last minute. The destruction of the relay results in 300,000 batarian deaths.
- Return Veetor’Nara to the quarians or not on Freedom’s Progress
- Recruit Grunt or not after Korlus
- Recruit Thane, Samara, Tali, any two, or all three
- Save Kal’Reegar or not on Haestrom
- Recruit Legion or not after the Derelict Reaper
- Upgrade the Normandy’s weapons, armor, and shields, or not
- Save the genophage cure or destroy it on Tuchanka
- Kill the thresher maw or not on Tuchanka
- Kill Morinth or Samara on Omega
- Exonerate Tali, let her be exiled, or reveal the truth on the Rayya
- [ME2: Kasumi: Stolen Memory DLC] Let Kasumi keep Keiji’s graybox or have her destroy it after Bekenstein
- [ME2: Zaeed: The Price of Revenge DLC] Pursue Vido or rescue the workers on Zorya
- [ME2: Zaeed: The Price of Revenge DLC] [If workers rescued:] Lose Zaeed’s loyalty, regain it, or leave him to die on Zorya
- Who to send on the Suicide Mission tasks
- Preserve the Collector Base or destroy it
- [ME2: Overlord DLC] Rescue David Archer or leave him
Mass Effect 3
The Reapers invade Earth. Shepard tries to rally the galaxy’s militaries against the Reapers, curing the krogan genophage and resolving the geth/quarian conflict in the process. In the meantime, the exiled human fleets are secretly building an ancient superweapon, the Crucible, which is rumored to be capable of wiping out the Reapers. It turns out that the Citadel is the key component of the Crucible, but the Reapers have relocated the Citadel to Earth orbit. The fleets counterattack the Reapers at Earth, allowing Shepard to reach the Citadel and activate the Crucible. In the process, Shepard meets the AI that created the Reapers and learns their true nature.
Six months have passed since the Bahak system was destroyed. Shepard is under house arrest for destroying the Bahak relay, and the Alliance is undecided on whether to prosecute for the deaths of 300,000 batarians. Communications go dark; a panel of Alliance admirals call Shepard forth for advice, and the Reapers invade Earth as Shepard speaks. Shepard and Admiral Anderson escape the attack and board the Normandy SR-2. Anderson reinstates Shepard, then stays to help coordinate the counterattack.
As the Normandy is leaving Earth to get help from the Citadel Council, Shepard is ordered by Admiral Hackett to divert to Mars. At Mars, Cerberus is executing scientists. Kaidan/Ashley is suspicious of Shepard’s Cerberus ties, but Shepard protests innocence. They enter the science facility and encounter Liara, who has discovered blueprints for a Prothean superweapon called the Crucible. A Cerberus operative is stealing the plans, so Shepard and team pursue. During the chase, the Cerberus operative is burned, revealing her to be an AI robot. The robot attacks Kaidan/Ashley, giving them life-threatening injuries that knock them out. Shepard disables the robot with a pistol and rushes Kaidan/Ashley to the Citadel for medical treatment.
At the Citadel, Kaidan/Ashley is stabilized, but the Council species are too concerned with their own territories to help Earth. The turian councilor, however, suggests appealing directly to the head of his government, the Primarch of Palaven, by hosting a war summit.
[ME3: From Ashes DLC] Shepard diverts to Eden Prime, where Cerberus is attempting to extract something from the Prothean ruins. The "something" turns out to be a living Prothean, Javik, who was in stasis for the last 50,000 years.
The Normandy travels to Menae, Palaven’s largest moon, to rescue Primarch Fedorian. Shepard reunites with Garrus, but Primarch Fedorian proves to be dead. Succession falls on Primarch Victus, so Shepard clears the way to Victus and successfully extracts him from the combat zone.
Victus declares that he will not assist Earth unless the pressure can be taken off of Palaven. He insists that, despite krogan/turian animosity, the krogan will be needed. Shepard holds the war summit, with Victus, Wrex [note], and an unnamed salarian dalatrass present. Wrex demands a cure for the genophage as his condition for helping, and reveals his knowledge that the salarians captured the fertile females which Maelon’s research produced and are holding them on Sur’Kesh.
Shepard and team land on Sur’Kesh to rescue the krogan women. It is revealed that Mordin [note] leaked their existence to Wrex. Cerberus attacks. Shepard fights their way through Cerberus forces and successfully rescues the last surviving krogan woman, a shaman who discarded her name and who everyone else takes to calling “Eve”. Mordin will need a tissue sample from Eve to synthesize the cure.
The Normandy travels to Tuchanka, secures an ancient anti-air gun, rescues the Primarch’s son, and defuses an ancient turian bomb placed as a back-up plan at the end of the Krogan Rebellions.
They next locate the Shroud, a salarian terraforming facility that protects Tuchanka’s habitability and an ideal place from which to disperse the genophage cure. However, a Reaper destroyer stands in their way. Shepard takes a detour through some ancient krogan ruins and encounters Kalros, an enormous thresher maw. Shepard sneaks under the Reaper to reach giant hammers that summon Kalros to the Reaper. Kalros successfully kills the Reaper. Mordin successfully disperses the cure, but dies when the Shroud facility crumbles due to damage sustained. If Maelon’s data was preserved in ME2, then Eve survives her ordeal.
The Normandy travels to the Citadel to meet with the salarian councilor, who has news about Councilor Udina. When Shepard arrives, the Citadel is under attack as Cerberus attempts to execute a military coup. Shepard fights their way to the salarian councilor, who is attacked by a powerful Cerberus operative, Kai Leng; the councilor’s life depends on Thane and/or Kirrahe having survived from previous games, but even if the councilor dies, Udina is revealed as the Cerberus mole that made the coup possible. Shepard then fights their way to Udina and the other councilors, but Kaidan/Ashley is unaware of Udina’s betrayal and they have a standoff. Shepard tries to convince Kaidan/Ashley to stand down, and the outcome depends on many, many factors; Shepard kills him/her if he/she cannot be convinced. Regardless, Udina dies and the remaining two councilors live.
The Normandy travels to meet with the Migrant Fleet, but the quarians are embroiled in a war to retake their homeworld from the geth. The quarians were winning, but the geth panicked and allied with the Reapers. The Reapers provided the geth with intelligence upgrades that turned the tide, at the cost of geth free will. Shepard teams up with Tali [note] to board a geth dreadnought and disable the intelligence-boosting signal. They discover that Legion [note] is being used to rebroadcast the signal to all geth. Legion is freed, and the quarian fleets regroup.
Shepard and team rescue Admiral Zaal’Koris, whose ship was downed. They also disable a squadron of geth fighters by helping Legion extract geth from a server; Legion convinces these geth to reject the Reapers and join Shepard’s side.
The Normandy locates the source of the signal, coming from an underground bunker. Shepard exposes it and points a targeting laser at it, allowing the Normandy to bomb it. However, the source turns out to be a destroyer-class Reaper. They sync the laser to the entire quarian fleet, and Shepard paints the Reaper’s vulnerable spot. The fleet repeatedly hits the Reaper until it dies.
With the Reaper destroyed, the geth have free will again, but have also lost the intelligence boost. Admiral Han’Gerrel presses his advantage, attempting to exterminate the geth. Legion begins uploading a permanent version of the intelligence upgrade, one that leaves the geth free-willed. Shepard must choose between siding with Tali, with Legion, or trying to navigate a peaceful solution. If Shepard sides with Tali, the geth are wiped out. If Shepard sides with Legion, the quarians are wiped out. If Shepard has enough persuasion and enough brownie points, they can convince Admiral Han’Gerrel to stand down, ending the war peacefully.
[ME3: Omega DLC] Shepard joins Aria T’Loak and liberates Omega from Cerberus control.
[ME3: Leviathan DLC] Shepard follows clues that lead them to the Leviathans, who provide vital backstory to the Reapers.
[ME3: Citadel DLC] Shepard is attacked by mercs who turn out to be working for a Cerberus-created clone of Shepard. The clone is jealous and wants to take over Shepard’s life. Shepard defeats the clone and optionally tries to save them, but the clone dies either way. Shepard optionally spares the ex-Cerberus operative who was assisting (and goading on) the clone.
The Normandy travels to the Citadel to receive critical information from the asari councilor. She reveals that the asari have hidden a fully-functional Prothean beacon inside a temple to the goddess Athame on Thessia. She hopes that it may contain critical information about the Crucible’s construction.
The Normandy travels to Thessia. Shepard and team fight their way to the temple, but they are attacked by Kai Leng. He defeats them and steals the required information.
The Normandy tracks Kai Leng to Horizon, the human colony world previously visited in ME2. Sanctuary, a purported refugee camp, is exposed as a Cerberus front; Cerberus is turning the refugees into husks to study indoctrination. Shepard arrives after Kai Leng has left, but encounters Miranda, her sister, and her father in a standoff [note]. There are many possible outcomes to the standoff, depending on Shepard’s persuasiveness, Miranda’s survival of ME2, Miranda’s loyalty in ME2, how many times Shepard has spoken to Miranda in ME3 and whether Kai Leng was mentioned in those conversations, and whether Miranda receives the unspecified Alliance resources she required earlier in ME3.
After Horizon, Shepard’s crew learns the location of the Cerberus Headquarters. When the Normandy travels there, it does so with the combined fleet that Shepard has amassed in the game through diplomacy. Shepard and team board the base to retrieve the stolen Crucible information. They fight their way through the base, encounter some interesting backstory, then fight Kai Leng to the death and successfully retrieve the information. The missing component of the Crucible is revealed to be the Citadel itself.
Unfortunately, as has by now become obvious, Cerberus is filled with indoctrinated agents top-to-bottom, and the Illusive Man already tipped his hand to the Reapers that he knew the Citadel was required. In response, the Reapers relocate the Citadel to geostationary orbit above London, England, Earth and begin preparations for the Harvest. The Citadel arms are closed, they need to be open for the Crucible to dock, and the only way aboard is via a beam in London that the Reapers use to transport their victims.
The combined fleet travels to Earth, beginning a military operation to get troops onto the Citadel. They successfully land troops in London and set up a Forward Operating Base. From the base, they push their way to the beam. However, a Reaper destroyer stands in their way. Shepard defends a mobile missile battery, then uses it to destroy the Reaper. Shepard and Admiral Anderson successfully reach the beam.
Inside the Citadel, Anderson reaches the controls first, followed shortly by Shepard, but the Illusive Man is there and uses some unexplained technology to control the other two like marionettes. The Illusive Man forces Shepard to shoot Anderson, as Shepard and Anderson try to talk the Illusive Man into realizing he is indoctrinated. If certain conditions are met, Shepard will succeed and the Illusive Man will commit suicide. If Anderson survived the conversation with the Illusive Man, then Shepard and Anderson will sit down and have a conversation before Anderson dies. The Crucible is docked but does not activate; Shepard passes out before they can determine why.
Shepard wakes in a chamber next to where the Crucible and the Citadel are docked together. The AI known as the Catalyst reveals itself, and explains its motives: it created the Reapers because synthetic life inevitably wipes out organic life, and the Reapers are there to preserve the organic life (in Reaper form) before the organic life is lost forever. It presents Shepard with three options:
- Destroy: Shepard can use the Crucible to destroy all synthetic life. This will end the war, but at the cost of destroying EDI, the geth, and any organic being whose life depends too much on technology (artificial organs, etc).
- Control: Shepard can use the Crucible to take control of the Reapers, uploading Shepard’s mind into a new AI that replaces the Catalyst.
- Synthesis: Shepard can sacrifice their body to rewrite both organic and synthetic life into a new hybrid form. This will prevent the "inevitable" conflict between synthetics and organics.
- Refusal: Shepard can refuse all three options and lose the war, leaving it to the next cycle to stop the Reapers.
- Free the rachni queen (again), or leave her to die
- Cure the genophage, or sabotage the cure so that it does not work
- Talk down Kaidan/Ashley, or shoot him/her
- Save the quarians, save the geth, or broker peace
- Ask Javik to touch the Echo Shard, or ask him to not do it
- Talk to Miranda on each of three occasions, or not
- Give Miranda access to Alliance resources, or not
- Save Samara, let her die, or let her die then kill her A-Y daughter
- The choice offered by the Catalyst