alternate timeline created by Peter Bishop's erasure, many of the events of John's life remain the same. He is still the partner of Olivia and still affected by the toxin. However, while Olivia is able to get Walter out his mental hospital to help him, John dies before a cure can be found. His death profoundly affects Olivia, leaving her even more isolated and cold than in the previous timeline. It is also suggested that the toxin which killed him may have been a disastrous attempt by ZFT to create human shape-shifters, although this is unconfirmed. Charlie Francis Charles "Charlie" Francis (portrayed by Kirk Acevedo; main: season 1–2; recurring: season 3) is an FBI Special Agent, who holds the position of a supervisor. He is close friends with John Scott and Olivia. Olivia often comes to him with requests for manpower and other resources. Charlie is later promoted to Second-In-Command of the Fringe division, making him the immediate subordinate of Broyles. In the season premiere of season 2, Charlie is killed by a shapeshifter who takes his place and burns his body in a hospital furnace. The shapeshifter maintains his identity for some time until it learns the location of Newton, after which Olivia is forced to kill it. Charlie's death weighs heavily on Olivia's conscience. She later receives a post-mortem message from him in the form of a series of seemingly random letters that arrange to form the first sentence Charlie ever told her. "You're gonna be fine." After original Charlie is killed in 2.01 and the shapeshifter is killed in 2.04, Charlie appears frequently in a special episode that airs between 2.10 and 2.11, a seeming continuity error that can be explained out-of-universe, as the episode was originally filmed with season 1 but was not released until January mid-season 2. The parallel universe version of Charlie Francis is alive and an agent of the alternate and more powerful Fringe division. The alternative Charlie ("alt-Charlie") shares many of the same traits as the prime version, although he is slightly more crass and has a small scar beneath his left eye. He also suffers from a parasite infestation in his body, a fate averted by the prime universe's Charlie in the first-season episode "Unleashed". Lincoln Lee Captain Lincoln Lee (portrayed by Seth Gabel; main: season 4; recurring: season 2–3, 5) is a team leader within the parallel universe Fringe division,