Cerberus
[Note: This bio contains spoilers about the rest of the game]
History since Mass Effect 2:
Since the finale of the Suicide mission:
Cerberus is financially devastated if Shepard destroyed the Collector Base.
Cerberus is receiving exponential financial increases from organizations that support the study of the Collector Base.
After the destruction of the Alpha Relay, TIM realized that the Reapers would reach the galaxy in mere months. TIM began to focus all of his efforts on expanding Cerberus to a size capable of remaining fairly anonymous, while having enough personnel to operate and secure bases of operations. Rather than having a dozen small research facilities devoted to studies scattered throughout the galaxy, Cerberus fired or relocated most of its agents to handful of larger research bases scattered throughout the galaxy.
The research and technology recovered from Project: Lazarus was relocated to an old Cerberus station known as “The Barn”. It is helmed by Henry Avel/Miranda Lawson. The Barn specializes in bio-engineering experimentation. Shepard can destroy the station by shutting down its power core (killing the defense AI known as “UDI”). This causes the base to be bombarded by local a local asteroid belt. Conversely, Shepard can keep the station intact so that he, Liara, or Miranda can utilize it.
The research and technology recovered from Project: Overlord was relocated to an installation in the Horse Head Nebula known as “Project: Aegis”. It specializes in the study of husk-technology for synthetic-engineering and experimentation, and is helmed by Gavin Archer, and a mysterious man known only as “The Director”. “Project: Aegis” is the base where Shepard first spoke to TIM in ME2. If Shepard did not shut down “Project: Overlord” in ME2, the base's main fighting force will be geth units, controlled by David Archer. Shepard can shut down the base's defenses, allowing for the Shadow Base (and STG forces – if available) to bomb the station. Alternatively, Shepard seize control of the base for himself, Liara, or Miranda.
Cerberus's best mercenaries, hired from organizations like the Blue Suns and Eclipse, are taken to a place known only as “The Spear”, a military complex located on a jungle planet. From there, most of the mercenaries are distributed to the Terminus systems to secure Omega, and a few other locations. The base houses roughly 1500 troops, who are retrained, bombarded with propaganda to fuel their hatred of the Alliance and the Council, and deployed on missions. The base is managed by an android (identical to Dr. Eva) pretending to be an actual human. Shepard can destroy The Spear by shutting down its mass effect fields and having the Shadow Base bombard it from orbit, or Shepard can use The Spear's communications system to trick its inhabitants into thinking that EDI is their local (android) overseer. Liara then deploys these troops throughout the galaxy to exterminate husk forces on human colonies.
Intact Collector Base
The Collector Base serves as TIM's new platform of operations in ME3. By researching the base's technology, Collector corpses, and ship grave yard, TIM was able to unlock the power within the ancient construct: highly advanced quantum entanglement technology that allowed him to disable entire colony communications; tamper with Reaper-to-husk interactions; and even damage a Reaper's hive-mind intelligence. TIM believes docking the Crucible to the Collector Base would allow the powerful Prothean A.Is to boost the Base's ability to effect the Reaper autonomy. TIM hypothesizes that the more Prothean A.Is the Crucible has, the more powerful its quantum entanglement communications will become – perhaps even being able to effect Reapers in every system.
Gaining control of the Collector Base comes with a steep price, unfortunately. The main control console inside the base was previously operable only by the Collector General, and as a result TIM began to experiment heavily on bio-engineering, synthetic-engineering, and cybernetic implants – looking for a way to activate the control console.
[Note: These experiments include the creation and release of the “Adjutants”. Their place of origin, Avernus Station – adjacent to the Collector Base – has been shut down and its personnel relocated to Omega, as a way to protect TIM, and limit suspicious traffic going to and from the Omega 4.]
As the Reaper war commences, TIM begins to panic. Desperate for a way to activate the Collector Base, his top scientists reason that Collector cybernetics (administered through nano-machinery) can allow TIM to activate the base's control console, and a Prothean Cipher (like the one in Shepard's head) would allow him to interface with the Collector Base. While TIM fails to secure Shepard's Cipher, he is able to implant himself with the necessary nano-machine technology. TIM knows that the only people able to activate the Collector base are Shepard and Javik, and tries to tempt them to join him on the Collector Base to end the Reaper war.
[Note: If the Collector Base was left intact in ME2, it opens up a third option for where to deploy the Crucible, near the end of the game. This changes the outcome of the Reaper war. Because none of the end-game-Crucible-deployment choices fall under a paragon-renegade spectrum, only the choices Shepard makes while performing the Crucible deployment actually matter]
Destroyed Collector Base
If the Collector Base was destroyed in ME2, then Shepard receives more military support from the Alliance and Hegemony for the final fight against the Reapers. TIM is captured during the assault on Cronos Station by Liara's Shadow Base. He is brought to the War Summit to answer for his crimes.
Missions involving Cerberus:
Tutorial – If aligned with Cerberus at the beginning of the game, TIM leads Shepard (via hacking security cameras, doors, etc).
Klencory: Beings of Light – Kai Leng's first appearance as he kills Kumun Shol. If Shepard is aligned with Cerberus, Shepard and Leng kill most of the people at the dig site (though not Liara).
Shadow Base – Dr. Eva, Cerberus spy-android, attempts to assassinate Shepard. She is stopped by either James Vega or Liara T'Soni. Shepard is no longer part of Cerberus.
Investigate: ExoGeni – Shepard infiltrates ExoGeni headquarters on Illium in search of Reaper artifacts. Cerberus is using ExoGeni as a proxy corporation.
Investigate: Reaper Technology – Shepard searches Feros in search of Reaper artifacts. Cerberus is testing Reaper technology on civilian population.
Investigate: Disturbance – Cerberus plants bombs in alien-owned shops on Citadel. Assassins, lead by Kai Leng, start shooting aliens in the streets. Shepard fights off the extremists, and pursues Leng.
Vault of Athame – After convincing the matriarchs to become more active in the war, Shepard enters the “Vault of Athame” to find the Prothean artifact hidden there for thousands of years. He is attacked by Yala, the asari who was flagged as a “geth security risk” with C-sec in ME2. She escorts Shepard to the vault, but Yala turns out to be one of TIM's android infiltrators.
Stop a Killer – Shepard pursues Leng through the keeper-tunnels, as the assassin attempts to kill a Citadel councilor. Leng escapes. Councilor is either killed/saved depending on game variables. Thane/Kasumi is either killed/saved depending on game variables.
Track a Killer – Shepard and Thane/Garrus/Jacob/Kasumi/Spectre ambush Leng in refugee apartments on the Citadel. Leng escapes wounded/fine depending on game variables.
Investigate: Cerberus Comms Station – Shepard and Jack take down a small Cerberus communications base, helping them locate the main bases of Cerberus.
Project Aegis – Shepard and Liara work to take down a Cerberus station devoted to the study of synthetic and mechanical engineering. Station can be saved/destroyed depending on game variables. Randall Ezno can be killed/saved based on game variables.
Spear Base – Shepard and Liara work to take down a Cerberus ground-base devoted to troop recruitment, training, and deployment. Jacob Taylor can be killed/saved based on game variables.
The Barn – Shepard and Liara work to take down a Cerberus station devoted the study of bio-engineering, alien experimentation, etc. Miranda Lawson can be killed/saved based on game variables.
Normandy: Disturbance – Shepard and Leng fight in the Normandy's cargo bay, after the assassin infiltrates the ship. Leng escapes, and blows up several other cargo bays. Joker can be killed/survive, depending on game variables.
Cronos Station – Shepard and Liara locate and assault TIM's main base of operations. Kai Leng killed. Jack/Miranda/Jacob/Kirahee can be killed, depending on variables. TIM arrested if Shepard destroyed the Collector Base. TIM not on Cronos Station if Shepard kept Collector Base.
Collector Base – If Shepard chooses to bring the Crucible to the Collector Base, the Shadow Broker and Citadel fleet attack the Cerberus beyond the Omega 4 Relay. The Crucible is brought to the galactic core to dock with the station. Reapers attack the Base, fleets, and Shepard. TIM and Shepard activate the Crucible, but TIM then fights Shepard. Ending depends on EMS levels.
Ironing out variables:
If Shepard kept the Collector Base, but was not aligned with Cerberus – Shepard cannot take over Cerberus at the end of ME3, and instead hands it over to either Liara, Miranda, or the Alliance.