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This game starts on board the Umbrella-owned ocean liner, Spencer Rain, which has been infested by the t-Virus stolen from Umbrella's Paris labs by bioterrorist and former-Umbrella employee Morpheus D. Duvall, and its secret B.O.W. cargo intentionally released. Morpheus holds the world hostage, with the US and China at ransom for $1 billion - if they do not pay the money, his followers will launch missiles from an undisclosed silo with the warheads being replaced with the t-Virus. Bruce McGivern, a member of USSTARTCOM's "Anti-Umbrella Pursuit Investigation Team", a U.S. government task force with the sole purpose of taking down Umbrella, is sent in. Alongside him is Fong Ling, sent by the Chinese MSS. Although they share the same goals and common enemy, their respective governments are against working together.

During Bruce's investigation, he is found by Morpheus and held at gunpoint on the foredeck. A surprise attack by Fong Ling with a grenade allows Bruce to escape into the ship, with Morpheus being injured in the explosion. He later infects himself with the experimental "t+G Virus" in order to avoid an otherwise-fatal wound. After a brief encounter with the mutated Morpheus in the cargo hold, Bruce escapes into engineering with the aid of Fong Ling. Regaining power to parts of the ship and discovering important items, the two gain access to the bridge - with Bruce killing the infected captain in the search - to find that the Spencer Rain is on a collision course with a nearby island. Running outside to escape the ship, Bruce is forced to fight Tyrant 091, which had escaped containment before Bruce's encounter with Morpheus. Once it is defeated, Bruce jumps into the ocean and swims to the shore as the liner is destroyed.

Briefly exploring the island, which is shown to contain an abandoned Umbrella facility, Bruce moves down into its waterways in search of Morpheus. Making his way through a series of underwater channels, he discovers that the island was used as a waste disposal facility for failed B.O.W.s until its was recently lost in a biohazardous outbreak. Deeper in the facility, Fong Ling has escaped from "Pluto", a failed experiment which Umbrella lost track of, later rejoining with Morpheus. It is at this point that they discover that the Chinese have given in to Morpheus' demands and have agreed to pay up, arranging for an orbital weapons satellite to kill Fong Ling with a targeted laser device. Bruce correctly deduces that the satellite is tracking a chip in her tattoo, and proceeds to dig it out with a knife. With the chip destroyed, the satellite ceases its attack. The two make their way to a storage facility to transport to the underwater Bio-Sphere where the missile silo is a part of, but Bruce is forced to fight Pluto before he can reach it.

With the Pluto defeated, the two their way down the elevator; Morpheus makes a sudden re-appearance, sending the elevator crashing to the sea floor. The two operatives survive the crash and explore the facility, finding that Morpheus' own bioterrorist organization has already been compromised by another t-Virus outbreak. Fong Ling is captured by Morpheus, who uses her to play a game with Bruce - try to save her, or abandon her to complete the mission. Bruce chooses to save her, allowing Fong Ling to provide logistical support as he searches for the missiles. Unfortunately, a greatly-mutated Morpheus prevents him from reaching the missiles in time, though further damage causes the G-mutant to expand to such a size that the missiles simply impact him and explode.

Bruce and Fong Ling are revealed to have escaped the underwater facility's destruction by use of an escape boat floating to the surface. With her own government believing her dead, Fong Long has nowhere to go but the United States; Bruce re-assures her and they kiss as US-STRATCOM sends in a helicopter to pick them up.