After Raiden and Pliskin disarm the C4 planted within Shells 1 and 2, Raiden receives shocking news from a now-mobile Peter Stillman. All the C4s (planted in places where severe damage could not be done to the Big Shell) were nothing more than diversions for the real explosives, large enough to disturb the structure's integrity. Additionally, the real bombs were programmed to activate after all of the smaller C4s had been disarmed. Although Raiden is able to disarm the Strut A bomb, after returning to the deep sea dock, the Strut H bomb detonates, killing Stillman. Pliskin, on the other hand, is able to survive unscathed. As Raiden prepares to leave Strut A, he is confronted by Fortune, who had been expecting to find somebody else. Nevertheless, she asks Raiden to "bring her death." Raiden, unable to harm her, can only evade her attacks. Shortly thereafter, Vamp arrives to inform Fortune that Fatman has gone rogue. Taking advantage of the distraction, Raiden takes another shot at Fortune, but the bullets are deflected and hit Vamp in the forehead and lower chest. While Fortune cradled Vamp in her arms, lamenting that she cannot follow him in death, Raiden escapes. However, moments later, Vamp awakens, having shrugged off this seemingly fatal attack.

With the bomb's countdown having already begun, Raiden heads to the heliport and neutralizes the explosive. He’s then confronted by Fatman, who professes his disinterest in the terrorists’ goals. Fatman is also suspiciously unaware of the ransom demands for $30 billion. His only wish is to surpass his former mentor, Peter Stillman, and become the most famous bomber in history by destroying the entire Big Shell. Challenging Raiden to stop him, he places multiple explosives in the area, utilizing his quick speed. Raiden is forced to neutralize each bomb with coolant spray while simultaneously fighting Fatman. The perseverance pays off, with Fatman collapsing from his injuries. After informing Raiden that he has yet to disarm the "biggest bomb in the place," Fatman dies. Raiden, however, discovers the last bomb, which had been hidden beneath Fatman’s body.