The mystery of the Tunguska event from the original game has been resolved, and playable characters Nina Kalenkov and Max Gruber have split up. Nina embarks on a cruise to Portugal and Max travels to Indonesia, but their separation does not last long. There has been an escalation of natural disasters around the world, and Nina's father Vladimir Kalenkov has been called upon to find out what is causing them.
At the start of the game a vicar, fleeing into his church, is killed over documents prophesying the apocalypse. He manages to get the documents into the hands of Bishop Parrey, a third playable character who is tasked with keeping the documents out of the wrong hands.
Like its predecessor, the game occasionally breaks the fourth wall. For example, when Nina is asked to pick up a gun she says that minigames have been forbidden by the lead designer.