Jia Jem Wearing Costume From Mass Effect 2

Shepard departs with the recruited members on a shuttle towards their next mission as the Normandy prepares the IFF for testing. However, after the IFF is activated, it emits a tracking signal and the Collectors are able to locate and board the Normandy. Joker is forced to give control of the ship to EDI - a potentially dangerous move. Gaining control of the ship, EDI pilots the Normandy away from the Collectors and rids the ship of all enemies, but the entire crew barring Joker is taken by the Collectors. Shepard's hand is forced - Shepard can either complete secondary missions and sacrifice the Normandy's crew, or immediately go through the Omega-4 relay to rescue them.
After traveling through the relay, the game may proceed in different ways. Depending on whether Shepard enters the Omega-4 relay quickly, has upgraded parts of the Normandy, and has earned the loyalty of team members, any combination of crew and team may survive the final mission, which ultimately influences Shepard's fate. After entering the relay, the Normandy enters a massive debris field littered with the wrecks of ancient starships that tried to navigate the Omega-4 relay. After a fight with the debris field's automated defenses, the Normandy encounters and ultimately destroys the Collector cruiser. The shockwave from the explosion, disables the Normandy and forces the ship to crash land on the Collector station. After boarding the station, Shepard and the team fight their way towards the center of the base eventually encountering the Normandy crew and the abducted human colonists. If Shepard delayed entering the Omega-4 relay, the Normandy crew will be harvested by the Collectors and Shepard will only manage to save a few of the human colonists. After rescuing the colonists and crew, Shepard continues to proceed to the large central chamber in the middle of the base and discovers that the Collectors have been constructing a new Reaper, made from the genetic material of the abducted humans and fused with the advanced technology of the Reapers. EDI postulates that the Reapers may be facilitating the Reaper equivalent of reproduction but remains unsure as to the Reapers' true motives. Shepard targets the weak points of the machine, which is in the early stages of construction, and it falls deep into the station core.
The Illusive Man then contacts the team and suggests keeping the station intact insisting that any information garnered will be valuable in the coming war against the Reapers and may provide new insight into their motives and capabilities. Shepard may choose to destroy the station completely by overloading its reactor, or use a radiation pulse to kill the remaining Collectors while leaving the station intact thus allowing Cerberus to take control of the station. Regardless of the choice, Shepard orders the team to evacuate to the Normandy. However, before Shepard can escape, the Human-Reaper larva manages to climb back up from the depths of the station and attempts to stop Shepard from destroying the station. However, the Commander manages to destroy the Reaper after a tense battle. As Shepard escapes the station, Harbinger claims that the team has only delayed the inevitable and that humanity now has the full attention of the Reapers. Shepard is then assisted onto the Normandy by any surviving team members. If all team members are killed, Shepard will attempt to reach the Normandy but before Shepard can climb onto the ship, the Collectors open fire and he/she will only have Joker to hold him/her. In this event, he will tell Joker to warn the Illusive Man before letting go of Joker's hand falling to his/her death. Depending on whether Shepard destroyed or preserved the Collector base, the Illusive Man will be displeased or pleased, respectively, with Shepard's actions with Shepard having the opportunity to cut the Illusive Man off and vowing to find a way to stop the Reapers with or without the Illusive Man's help. Later, while the ship is being repaired Shepard or Joker is seen standing over the caskets of the dead team members should the team have suffered casualties. Otherwise, Shepard is silently greeted by his teammates and crew. In dark space, a Reaper (presumably Harbinger) is seen awakening from hibernation. As it awakens, the dark void surrounding the Reaper is illuminated by hundreds or thousands of Reapers. The final scene shows the Reaper fleet descending upon the Milky Way galaxy, setting the stage for Mass Effect 3.