The plot follows around an agent called Ark Thompson who was requested by Leon S. Kennedy to infiltrate an Umbrella facility. He managed to breach security in the Umbrella-controlled Sheena Island by impersonating the leader of the Umbrella facility, Vincent Goldman.
Goldman, after being told of Ark by a small boy, Lott Klein, causes an outbreak intentionally, causing him to lose his memory, and his train of thought. Thus, the game begins with Ark not remembering who he is.
Ark's journey through the island slowly leads him to believe he is Vincent Goldman and is responsible for the horrible experiments conducted on the children brought to the island. Ark slowly learns of Vincents actions and encounters a small boy named Lott and his sister Lily Klein.
They at first run and attempt to attack Ark, but they slowly learn to trust him after Ark attempts to save Lott for his sister. Making his way through the city, and into the Tyrant Plant, Ark encounters multiple B.O.W.'s on the island he must combat. This include zombies, cereberi, lickers, hunters, and T-103s.
In the Tyrant Plant, Vincent attempts to kill Ark, but is instead killed by the experimental Tyrant Hypnos-T Type. After a brief battle, Ark appears to have killed the creature and continues on.
Eventually the boy and his sister are reunited and proceed to escape the island with Ark, who by now has remembered who he was and why he was on the island. They proceed to an elevator that takes them to a helipad for escape.
The Hypnos-T Type Tyrant has since then changed forms and attacks Ark again, after a small battle, the creature finally turns into its third and final form. After a battle on the helipad, Ark finally appears to have killed the creature and proceeds to the helicopter for escape. As the three fly off, the creature tries to bring down their helicopter and jumps onto it, Ark then fires two missiles at the creature, finally killing it for good.
The game ends with a scene of the helicopter flying into the distance, Ark telling the children that he doesn't know what will happen next, but can keep flying as long as they have fuel.