The intro describes the effects on Earth in the anti-matter universe after Snow, Neku, Vic, James and Ender escaped anti-Pelvanida with the death of Tardigan. With their knowledge, they revolutionized technology and integrated into society, but died abruptly several years later. As those who encountered them met similar early deaths, the world slowly realized that they'd brought a highly infectious plague with them. Soon the plague threatened to wipe out all of humanity within the next few years.
The player assumes the role of a team leader who manages to reactivate the Einstein-Rosen Bridge using the remaining fuel from the SS Hawkeye. Traveling alone to the matter universe, the traveller finds themselves in the New Pelvanida bridge room, near a mop and bucket. After obtaining a vial of stabilized francium from the supply closet, they blow the door open and reach a corridor. From the corridor they use a portion of the mop handle and tape from the receptionist's desk in the lobby to fool the thumbprint scanner locking the infirmary. After reviewing the infirmary's medical texts and discovering the recipe for the cure, the traveller visits the electrician's closet an obtains an Arc Flash suit to protect himself from the turret in the control room. They manage to reactivate the bridge, but due to failure to enact safeguards, the computers warn that the bridge will irreparably meltdown in thirty seconds. Depending on the player's choice, the traveller either returns with the cure to their home universe or chooses to remain in the matter universe.