The Lazarus Project

Jacob Taylor.

Miranda Lawson.

Commander Shepard awakens in the year 2185 aboard a Cerberus space station, a research facility of the Lazarus Project, which is under attack by hacked security mechs. After the Commander aids Cerberus agents Miranda Lawson and Jacob Taylor in escaping, Shepard is taken to a headquarters of Cerberus and granted an audience with the Illusive Man, leader of the infamous experimental research organization,who explains that Shepard was revived and "upgraded" in return for the Commander's aid in combating a new threat in which human colonies have been attacked, their colonists deemed missing.

The Illusive Man.

One Month Later...

An uknown ship attacks and destroys the Normandy.

2183, one month after the Battle of the Citadel, while on patrol to locate and destroy any remaining geth, the Normandy comes under attack by an unknown assailant. The ship suffers extensive damage, forcing the crew to evacuate via escape pods. Joker continues to pilot the ship despite the received damage to it and is rescued by Commander Shepard, who drags Joker out of his seat and into an escape pod. Before the Commander may board the escape pod, however, the Normandy is attacked once again and Shepard is sent flying amidst a series of explosions. Debris slices through Shepard's suit and air vents out. Shepard asphyxiates and dies; the Commander's body is seen entering the atmosphere of a nearby planet.

The Aftermath

Commander Shepard.

Garrus Vakarian.

Kaiden Alenko.

The Council, in recognition of humanity's salvation of the galaxy, allows the humans a seat on the Council. Shepard nominates  Anderson as the Human Councilor, and they prepare to combat the Reapers with the Alliance Fleet at the forefront. Anderson is given the position.

Liara T'Soni.

Tali'Zorah nar Rayya.

Shepard leaves the Citadel aboard the Normandy, intending to find a way to stop the Reaper invasion.


The Battle of the Citadel

 Shepard and the team manage to get out of the overturned Mako and use the nearby malfunctioning Avina terminal to get a sit rep. Saren is heading toward the Council Chambers and the whole station is infested with geth. The squad tries taking the elevator to the Citadel Tower, but it stops halfway when Saren locks down the station's systems. Shepard tells the team to suit up and blows out the elevator's glass with a shot. They have to walk the rest of the way in zero gravity with their boots magnetized.



Council Chambers in the Citadel Tower.

Meanwhile up in the Chambers, Saren—angrily shooting keepers as he goes—reaches the central console and uses it to take control of the Citadel. As Sovereign gets closer, crushing the Citadel Fleet ships in its path, Saren closes the Wards, creating an impenetrable shell around the Reaper and the Geth Dropships already inside. Sovereign settles on top of the Citadel Tower, preparing to open the Citadel Relay once Saren transfers full control.



Geth Dropship.

Elsewhere Shepard and the team are fighting for their lives against the geth and Saren's krogan warriors out on the Citadel's exhaust plains, trying to get to the Chambers. A geth dropship appears and starts unleashing shock troopers on them; Shepard activates the Citadel's defense turrets, and with their cover fire, takes the dropship out. Further along they run into several powerful geth turrets and have to use cover to get close enough to destroy them, or manage to sneak down a side route where Krogan Battlemasters are waiting. Eventually they reach a maintenance hatch that leads down into the Council Chambers, now burning and full of Saren's geth. The stairways provide some cover as the team fights towards the central console.

Krogan Battlemaster.

At that moment Saren appears and throws a grenade. Shepard's team are blown aside while the commander takes cover close to Saren. He urges Shepard not to be a fool—everything is lost if Shepard continues resisting Sovereign. Sarenboasts that his faith faltered but Sovereign has implanted him, made him partly synthetic, perfect. This is the future of organic life. Shepard can't believe Saren allowed Sovereign to implant him. Shepard can attack Saren straight away, or try talking him down—the more Shepard talks, the more Saren is convinced, but his Reaper implants cause the turian intense pain when he begins to agree with Shepard. With enough convincing, Saren thanks the commander for freeing him before shooting himself in the head. Whether Shepard kills Saren or Saren kills himself, he then falls to the bottom of the Chambers, falling through the glass floor and being impaled by a large shard.

　

Using the central console, Shepard uploadsVigil's program and gains control of the Citadel. With advice from the team, Shepard opens a communication channel and gets Joker... who has the Fifth Fleet just waiting for the commander's word once the mass relays are unlocked. Shepard has to decide between sending the Fleet to defend the Destiny Ascension and save the Council, letting the Council die, or focusing on Sovereign. Once the orders are given, Joker brings the Fleet through the nearby mass relay as Shepard opens the Citadel's ward arms.

The Destiny Ascension leading the Fifth Fleet into battle.

As the Fleet engages the ships outside—geth dropships and Sovereign itself—Shepard tells the squad to check Saren and make sure he's dead. They drop down to the bottom of the Chambers—one coldly shoots Saren in the head, while the other confirms the kill to Shepard. Suddenly Saren's body begins to twitch as his implants fire up, burning his flesh away until he is a cybernetic construct like a Husk, completely possessed by Sovereign. The shockwaves from his transformation cause the platform to collapse and Shepard falls into the bottom of the Chambers. The squad fights back against the creature, but it is fast and deadly.



Saren Husk.

Outside, the Normandy is leading the attack against Sovereign. The Reaper unleashes a terrible weapon that burns through several Alliance ships, but the Fleet is slowly getting the upper hand. As the squad finally destroy the cybernetic creature and it burns away to ashes, Sovereign begins to weaken under the Alliance attack and releases its grip on the station. A blast from the Normandy is the coup de grace and the Reaper is destroyed.

　

In the Chambers, Shepard looks up to see a huge piece of debris from the Reaper heading straight for the Tower. The commander yells for the squad to take cover, just as it hits.



Sovereign is destroyed.

Much later, rescuers enter the Tower looking for survivors. Under a pile of rubble they discover Shepard's team... two of them, badly wounded but alive. Leading the rescuers, Captain David Anderson helps them out, assures them that it's all right, and asks where Commander Shepard is. One of the squad looks sadly across the Chambers, where the Reaper debris has crashed into the floor. It would have crushed anyone standing under it. The rescue team helps the squad out of the Chambers, reluctantly believing Shepard died in the crash. Anderson looks back—to see someone moving. Commander Shepard, with an injured arm, manages to climb out from behind the debris, limps toward them, and smiles.

Ilos



Shepard and Liara.

After Liara spends a night in the Commander's quarters, Joker announces that they're about to pass through the Mu Relay, and they soon arrive at Ilos. Shepard sees that Saren has already arrived with a fleet of geth dropships, though the Normandy's stealth system is keeping them safe for now. Navigator Pressly picks up some readings on the planet confirming Saren's presence. However, they can not find a landing zone. Shepard suggests dropping the Mako but they need about 100m of open terrain for a safe drop and Pressly can only find at most 20m. Joker insists that he can do it. The Mako is successfully dropped outside an ancient bunker, but Saren and his geth have already made it inside, shutting a heavy security door behind them.

　

Vigil, the Prothean VI.

Shepard looks for ways to get to the other side of the bunker doors. After fighting through the geth left on guard, Shepard and the squad find a security station and reopen the bunker doors. While in the control room, Shepard discovers an ancient Prothean recording which is heavily damaged. The Cipher allows Shepard to make out some of the words—it's another warning about the Reapers but it's just too broken up. They return to the Mako and enter the bunker. After driving past cryogenic stasis pods, all apparently shut down, Shepard sees a mysterious energy barrier. As the Mako reaches the barrier, another barrier appears behind them, trapping the squad inside. The only way out is through a door at the side of the wall. After heading down an elevator, Shepard finds an ancient Prothean VI named Vigil, who has information Shepard needs to stop the Reapers.

A keeper at work.

Vigil unveils a startling revelation. The Citadel is actually a trap; a huge mass relay linking to dark space, outside of the galaxy, where the Reapers are waiting. The keepers are presumed to be one of the earliest races to be indoctrinated by the Reapers, who set them the task of maintaining the Citadel and activating the Citadel Relay when Sovereign signals them. It is also revealed that Sovereign is the vanguard of the Reapers. After every Reaper attack, they leave behind one of their kind to act as a vanguard and to monitor the development of the galaxy's races. Once the galaxy's races are sufficiently advanced, the vanguard will activate the Citadel Relay and usher in the next genocide. The reason the Reapers harvest the galaxy of all advance organic life approximately every 50,000 years is currently unknown. According to Vigil, not even the Prothean scientists could comprehend why they do it. They may be driven by goals that organics find impossible to understand. Once the galaxy is harvested, the Reapers return to dark space to hibernate and conserve energy. In this state, they are apparently vulnerable, so they always seal the Citadel Relay behind them.

The Relay Monument.

When the Reapers last attacked about 50,000 years ago, their genocide of the Protheans lasted for centuries. Ilos' personnel hid in cryogenic stasis, watched over by Vigil. However, as his energy reserves ran low, he followed a contingency plan by shutting off pods of non-essential personnel to conserve energy, hoping that when the time was right, he could safely open the pods. In the end, Vigil managed to save a dozen scientists. The few remaining Protheans on Ilos traveled to the Citadel through the Conduit—a small prototype mass relay, built by the Protheans, enabling a one-way link from Ilos to the Relay Monument in Citadel Presidium. The survivors altered the signal that the keepers respond to and prevented them from activating the relay to dark space.

Vigil also explains that if Sovereign assaults the Citadel alone, the combined power of the Citadel Fleet would be enough to defeat the single Reaper. However, if Sovereign is able to direct an agent to go through the Conduit as a back door and transfer control of the Citadel back to Sovereign, it will be able to manually activate the Citadel Relay and bring in the rest of the Reapers. Sovereign had possibly planned this for centuries after discovering the Protheans' sabotage plan.

The Conduit on Ilos.

Vigil gives Shepard a data file that will give the commander temporary control of the Citadel to stop Sovereign. After leaving Vigil, Shepard heads through the archives, down into an old aqueduct guarded by geth, and reaches the Conduit. Saren had already gone through, leaving geth to stay guard.

Meanwhile, Sovereign begins its assault on the Citadel, escorted by a large geth fleet. The commander of the Destiny Ascension attempts to close the Citadel but the station doesn't respond—the operators at Citadel Control are all dead. Saren has begun his attack from within.

Back on Ilos, Shepard sees the Conduit is closing fast. Rushing to the Conduit, Shepard evades the geth in the process and drives the Mako through, just before the relay closes.

Grounded



The Citadel.

Thanks to the undamaged beacon on Virmire, Shepard's Prothean vision is now complete. During the debrief, Liara touches Shepard's mind to interpret it fully. The vision was a distress call intended to warn the Protheans about the Reapers. Liara realises that the landmarks in the vision are on Ilos, a planet she has studied as part of her Prothean research. Ilos had been impossible to reach because it was only accessible through the Mu Relay, which is why Saren needed the Relay's location from Noveria. After the debrief, Joker has a message for Shepard from the Council: they're putting together a massive multi-species effort to face Saren.

　

The Citadel Council.

Thrilled the Council are finally taking this seriously, Shepard returns to the Citadel, wanting to personally lead the assault. But once back at the station, Shepard discovers the Council are only putting up a blockade around the Mass Relays to stop Saren reaching the Citadel. Neither they nor Ambassador Udina believe Shepard's story about the Reapers and they refuse to send a fleet to Ilos. The Mu Relay is in the Terminus Systems and a Citadel fleet there could start a war. Shepard knows the Normandy's stealth systems can get them there discreetly, but the Council are getting tired of Shepard's insistence that the Reapers are the real threat. Udina, wanting to make nice with the Council, locks out the Normandy's systems and grounds the ship.

Captain David Anderson.

Frustrated, knowing Saren is close to finding the Conduit and they're losing time, Shepard is grateful when one of the squad offers support, but a real breakthrough comes when Captain Anderson gets in touch, asking Shepard for a discreet meeting at Flux. Anderson believes the commander's story and knows the Normandy is the only ship that can get Shepard to Ilos. He is going to unlock the Normandy's systems, allowing Shepard to steal the ship and take her to Ilos. Shepard is concerned that Anderson will be arrested and charged with treason—or worse—but Anderson sees his future as a small price to pay for stopping genocide on a galactic scale. Shepard goes to the Normandy and waits with Joker on the bridge. With Anderson's help the Normandy's systems are unlocked and they escape the Citadel, heading to Ilos.

Virmire



Captain Kirrahe.

The Council contacts Shepard with a possible lead. A salarian espionage team on Virmire, investigating reports of Saren's activities, has sent a mission-critical transmission that was almost lost in static. Shepard heads to Virmire and meets the leader of the salarians, Captain Kirrahe. They have found a breeding facility for krogan that Saren is using to create an army.

Kirrahe, realising he's not getting the reinforcements he needs, asks for Shepard's help destroying it and they develop a plan. While the salarians distract Saren's geth, Shepard will take a team around the back and plant a nuclear device that will wipe out the facility. Kirrahe asks Shepard for a squad member to help him coordinate the attack—Shepard sends Ashley to help the salarians, but must also deal with Wrex, who is furious that Shepard is willing to destroy a cure for the genophage, a salarian bioweapon which makes Krogan breeding next to impossible. The disagreement becomes a Mexican standoff, ending when Ashley guns Wrex down from behind.

Wrex turns on Shepard.

Sovereign speaks.

Leading the strike team, Shepard, Liara, and Garrus reach the facility, but discovers its main purpose is not to breed krogan, but to study Sovereign's horrific indoctrination effect. In Saren's private lab, the team finds another Prothean Beacon that gives Shepard another vision, and they are confronted by a hologram of Sovereign itself, which is not a Reaper ship but an actual Reaper.



Explosion on Virmire.

Shepard manages to get the nuke set up across the facility only to get a call that the salarians are being attacked with heavy losses. The commander takes a group to help them but as they leave, the geth start attacking the nuke site and Shepard has to choose: both Kaidan and Ashley are in trouble and there's no time to save both. Shepard goes back to Kaiden, as he is in possession of Kirrahe's nuke, and then brings reinforcements in, only to be confronted by Saren. He tries to make the commander join his cause but Shepard refuses, fighting Saren off. Saren gets away and the team board the Normandy, escaping Virmire as the nuke destroys the facility, killing much of Kirrahe's team, including Ashley Williams.

Having lost two squad members to Saren's forces on Virmire, Shepard retreats into space to assess the situation. Captain Kirrahe and his surviving unit is also taken aboard the Normandy.