See also: Fringe (season 2)
Much of Season 2 focuses on the alternate universe. It is established that Peter from the present universe died from a childhood disease; Walter, already with knowledge of the other universe, crossed over hoping to save that Peter, but instead was forced to bring him back to his universe, and kept this knowledge to himself. While Walter was aware that his crossing created "soft spots" in his universe, he is unaware that more significant and dangerous singularities occurred in the alternate universe as ripple effects of his crossing. As a result, the alternate Walter (referred to as "Walternate"), now U.S. Secretary of Defense, leads a more powerful Fringe division in the alternate universe to deal with further breeches led by Walter's alternate, including the development of shapeshifting technology that could travel to the present universe, and the means to communicate with its agents once there. Meanwhile, the Observers warn Walter that he should not let Peter return to the alternate universe as to avert a great disaster to either universe; Bell later describes this "great storm" to Olivia when she arrives.
A shapeshifter from the alternate universe kills Olivia's partner, Charlie, and under his form, finds the location of one of their agents, Thomas Jerome Newton. Newton, using information stored in portions of Walter's brain which Bell had purposely removed at Walter's request, devises a means to connect the two universes in order to allow Walternate across. As the Fringe division attempts to stop Newton, Olivia is forced to recall her Cortexiphan-induced ability to see objects that originated in the other universe, and comes to discover the truth about Peter. Walter urges her not to tell him as he wishes to tell him himself but is struggling in how to approach it. However, as a result of Newton's actions, Peter learns himself about his past and runs away to think to himself. Peter encounters Walternate, who offers to bring him back home, and Peter accepts.
Urged on by the Observers, Olivia and Walter manage to travel to the alternate universe, where they encounter Bell while avoiding capture from the alternate Fringe team. While Walter and Bell make peace with each other and prepare for a return trip to the present universe, Olivia is able to intercept and detain the alternate Olivia ("Bolivia") and pose as her to rescue Peter. Peter, realizing that the alternate Walter is seeking to use his personal bio-signature for a strange device, willingly goes with Olivia to return. In the process of preparing for the return trip, the group encounters the alternate Fringe team, and in the midst of the firefight, Bolivia is able to pass herself off as her doppelganger. Bell sacrifices himself to provide enough power for the three to return, unaware of Bolivia's switch. Peter and Walter reconnect once home, while Bolivia makes contact with the alternate universe, assuring them of her infiltration. In the season cliffhanger, Walternate is shown holding Olivia in a sensory deprivation cell in the alternate universe.