After Commander Shepard is killed in a Collector attack that results in the destruction of the SSV Normandy SR1, Cerberus is able to recover Shepard's corpse with the help of Liara T'Soni. The Illusive Man creates and funds the Lazarus Project, pouring virtually unlimited resources into the belief that only Shepard can stop the Reaper threat to humanity, as the Council stands idly by. The exorbitant project took 2 years, and over 4 billion credits. Undertaken by the Lazarus Cell which was headed by Miranda Lawson and her assistant Wilson, it involved attaching cybernetic implants to reconstruct the Commander's skeleton, reconstruction of the skin, and fluids to restart the blood flow and internal organs. However, the one thing that the Illusive Man refused to do was implant a control chip in the Commander's brain, fearing that it may affect Shepard's personality and abilities. As part of the project Shepard undergoes facial reconstruction, and a partial loss of prior abilities and talents. This explains why those who import a character from Mass Effect are able to change their appearance or class. However, this process does not change the Commander's sex. The project proved to be a success in 2185, when Shepard managed to regain full neurological activity.
During the assault on Cronos Station, a few records of Project Lazarus are discovered.
- The Lazarus Project is a reference to Lazarus of Bethany, who in the Bible was restored to life by Jesus Christ, four days after his death.
- Talking to Miranda early on in the game reveals that she pushed for a control chip to be implanted within Shepard's brain, but was overruled by the Illusive Man (who insisted that Shepard be brought back exactly as the Commander had been).