On July 23, 1998, STARS Bravo team is sent in to investigate a series of grisly murders in the Arklay Mountains region outside of Raccoon City. On the way to the scene, Bravo's helicopter malfunctions and is forced to crash land in the forest. Luckily, there are no fatalities. The team soon discovers an overturned military police transport truck, along with the mutilated corpses of two officers. The team soon splits up and Bravo team's field medic, rookie member Rebecca Chambers, stumbles upon a train suspiciously stopped in the middle of the forest; the Ecliptic Express.
Soon thereafter, she discovers that it is infested with zombies. Rebecca begins to wonder what she has got herself into. After a little exploration, she teams up with the man the military police were escorting to his execution; former Marine Billy Coen and the two explore the remaining train compartments whilst combating the now-zombified passengers, swarms of strange leeches, and a mutated scorpion.
As the train begins speeding out of control towards a cliff, the two manage to apply the brakes and divert its course towards an abandoned research and training centre. They investigate the underground facility, being forced to defeat the Umbrella Corporation's experiments: mutated insects, spiders, and primates. During their navigation, Billy Coen reveals that his unit was forced to kill the innocent civilians of an African village in the midst of a civil war against his wishes, and he soon found that their actions were based on false information.
They discover that the former operator of the facility James Marcus, along with Ozwell E. Spencer and Edward Ashford, discovered a virus (called the Progenitor or "mother virus") which, when combined with the ebola virus, created a strain that, despite being photosensitive, caused rapid mutations. Ashford originally wanted to use the virus to help the handicapped through its regenerative effects, but after his death Spencer and Marcus began research on its applications for bio-weapons, combining it with leech DNA which eventually led to the formation of the T-Virus. After a showdown with a gigantic bat inside a church outside the facility grounds, Billy is attacked by an infected primate and becomes lost inside an underground laboratory. While searching for him, Rebecca briefly meets Enrico Marini and then fights a released Tyrant before finally finding him washed up on a walkway. After fighting the Tyrant together, the two eventually meet Marcus. It is revealed that both Wesker and William Birkin were oblivious to the cause of the outbreak in both the Ecliptic Express and the Spencer Mansion, and that the real culprit was Marcus, an employee of Umbrella who operated the facility until his assassination by his two right-hand men, Wesker and Birkin, on the orders of Spencer. During his dying moments, his pet queen leech entered his body and reproduced exponentially over a few years to absorb his DNA and memories, giving him a new life. Marcus proceeds to split into a mass of leeches, before chasing Rebecca and Billy through the facility.
As was threatened earlier on, Birkin activates the self-destruct system as Marcus, transformed into the Queen Leech, Rebecca and Billy continue to fight. After being injured due to a brief exposure to sunlight, Marcus is paralysed when the overhead entrance to the laboratory is opened just as the sun rises. Rebecca throws Billy her pistol and he delivers the final shot to the Queen Leech.
As the facility crumbles, the two escape into the forest and come to a halt on a hill overlooking the Spencer Estate. They salute one another after Rebecca declares Billy "officially dead". Each goes their own way, with Rebecca heading towards the mansion to investigate the whereabouts of Bravo team. The screen fades to black as a far-off gun shot is heard.
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