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Summary	Plot	Gameplay	Development	Marketing	Reception	Credits	Gallery	Translation errors	Further notes

"A midwestern town in America: Raccoon City A solitary island far off in the sea: Rock Fort Island. An island that would become the second 'Raccoon City': Sheena Island. There are still many unanswered questions about these seemingly-unrelated yet intensely-traumatic events. Though it is believed that the international enterprise, Umbrella, was somehow involved, little is known as to the origin of this faceless corporation. When was it established...? By whom? And how was the t-Virus created? To uncover the truth, we must dwell deeper into the events which transpired in the beginning, before the Mansion Incident." — Prologue

On the evening of July 23, 1998, an Umbrella-owned train, the Ecliptic Express, travels through the Arklay Mountains, where several Umbrella facilities are located. Observed from a mountain top by a mysterious man singing a choir song, the train is attacked by a swarm of leeches, which break through the windows and attack the passengers. Two hours later, Bravo Team flies over the same mountains. As part of the S.T.A.R.S. police special forces group, Bravo Team's mission is to investigate a series of unexplained cannibalistic murders and animal attacks that have been occurring in the region. However, their helicopter malfunctions and crash-lands. While RPD pilot Kevin Dooley stays behind to fix the helicopter, Bravo Team searches the area and discovers a wrecked Marine MP vehicle. The drivers are dead, and Marine 2LT Billy Coen, who was being transported as a prisoner, is missing. Assuming that Coen killed his guards and escaped, Captain Enrico Marini orders the team to search for him.

While searching the Raccoon Forest, Rebecca Chambers, the team's medic, discovers that the Ecliptic Express has come to a halt and its lights are out. Upon further investigation, she finds bloodstains on the seats and is suddenly approached by a passenger who awakens from his slumber. More men soon surround her, but she manages to escape and heads towards the front of the train where she locates Billy. However, Billy is uncooperative and refuses to be detained, armed with a handgun he took from the MPs. Suddenly, Edward Dewey a Bravo Team member, jumps through the window, but he is seriously injured and passes out after being attacked by "zombies and monsters." Zombie dogs soon appear and chase after him. Marini contacts Rebecca on the radio, unaware of the monsters, and informs her that he has found further documents suggesting that Billy was sentenced to death for the murder of 23 people and was taken to a psychiatric hospital. While exploring the upper deck of the train, Rebecca encounters another man in a dining room who, upon her inquiry, transforms into a pile of leeches, which had been mimicking human form. Billy saves her, and they begin to trust each other. Later, they witness a strange man on the mountain, surrounded by leeches, singing.

The train begins to move in what is discovered to be an operation by the Umbrella Security Service's Delta Team. They have been tasked by Drs. Albert Wesker and William Birkin to move the train for investigation into the attack. The men are then attacked by leeches and quickly turned into zombies, leaving no one in control of the train. As it moves through the mountains, the train picks up speed. Realizing they might derail, Billy and Rebecca manipulate the brakes on the front and rear of the train, killing Zombie Edward in the process. The train slows down, but it is too late to prevent an accident, as it drives through a cliff and into an underground train station, derailing in the process.

Billy and Rebecca escape the derelict train and find themselves in a large facility, which used to be an Umbrella Pharmaceuticals training school. They discover evidence of biological weapons development led by Dr. James Marcus, the school's director and Umbrella co-founder. Birkin and Wesker monitor their movements via CCTV, but the mysterious man from the facility's security room intercepts the feed and accuses Birkin and Wesker of betraying Marcus and contaminating the Arklay Laboratory and the train.

As Billy and Rebecca explore the training school, they uncover disturbing evidence of what happened here both in the 1970s and recently. Although it was built to oversee the training of gifted teenagers recruited by Umbrella, evidence points towards Marcus deliberately using the children as test subjects in inhuman bioweapons research. This turned them into Zombies, with a two-level basement containing a torture chamber covered in dried blood. Zombies roam the halls of the school, some of them being those children left alone for twenty years. Others belong to Birkin's investigation team, consisting of USS and technicians sent recently to refurbish the school for reopening.

Evidence of a dispute between Marcus and Umbrella's CEO, Dr. Oswell E. Spencer, is also discovered, pointing to Spencer trying to steal Marcus' research on the Progenitor Virus and the t-Virus Project. The mysterious man spots Rebecca on the CCTV and sends out Marcus' Eliminator B.O.W.s to kill her. One tracks her down and bites her in the torture chamber, and during this confrontation, the floor gives way. However, she is soon rescued by Billy.

During their navigation, Rebecca finally gives in and demands Billy tell her the truth about what happened to him. He explains that his Marine unit suffered casualties due to faulty intelligence when searching for a guerrilla base in an African jungle. His CO ordered them to fire on villagers, but he refused to take part. He was then scapegoated by the unit, with a court-martial finding him guilty to cover up the other scandals.

Meanwhile, Birkin and Wesker begin their own plan to deal with the mysterious man, whom they believe is Marcus brought back to life. They consider him a significant threat and decide to activate the facility's self-destruct device to blow up the training school and the man with it.

Billy and Rebecca then proceed to a dilapidated church, where they take an elevator down into an even more dilapidated laboratory used by Marcus for his t-Virus research. Here, they find even more evidence of Marcus' cruel research. When Rebecca ventures upstairs, she discovers an auxiliary research room filled with human victims preserved in fluid-filled capsules, with other capsules containing harvested organs. In the nearby operating room, there is a mutilated "thing," and the morgue is overfilled, with body bags being casually dumped aside. The shelves are stocked with poisonous chemicals used in Marcus' research, and the operating room is covered in blood from his surgical procedures on the teenagers. Once again, they encounter the Zombified investigation team, with signs pointing to a violent confrontation beyond just leeches, including an infected man trapped in a gas chamber that someone switched on.

Downstairs, Billy investigates Marcus' study and discovers a photograph of him in his younger years, looking exactly like the mysterious man. He theorizes that the man is Marcus's son or grandson.

Ready to leave the laboratory on an underground cable car, Billy and Rebecca are attacked by one of Marcus's Eliminator B.O.W.s. During the fight, Billy falls down a ledge and into an underground stream.

Heading out on her own, Rebecca makes her way to the Umbrella Chemical Plant, located downhill from the training school. Signs point to it also having been attacked by the mysterious man's leeches recently, and the facility's personnel are strangely absent. Heading down a large train elevator, Rebecca reaches NEST, the site of Birkin's own bioweapons research. There, she runs into none other than Enrico, who has infiltrated NEST through the Arklay Laboratory's subway tunnel. He is confused as to why the rest of the team isn't there and decides they should head back to find where they went. Rebecca refuses to go, needing to find Billy. Enrico reminds her that he can't be saved either way, but he gives in and lets her stay to find him while he returns to the lab. Soon after, Rebecca is confronted by the T-001, Umbrella USA's Tyrant prototype, which has been released by the mysterious man, but she quickly knocks it out.

Heading into an adjoining water treatment plant, Rebecca finds Billy being dragged by the currents of the underground stream. As they move through the plant, they discover that the workers have also been turned into zombies, due to the combination of the mysterious man's leeches and NEST's unsafe biowaste disposal practices. After finding Billy washed onto the decking, Rebecca helps him up. When he regains consciousness, he notices that the decking is covered in skeletons, which leads him to conclude that Marcus had also dumped them in the water.

As they continue to explore the treatment plant, they finally come face to face with the mysterious man himself. He reveals to them his true origins: he is the Queen Leech, a mutant test subject created by Marcus in 1988. Marcus was killed by the USS on Spencer's orders, and Birkin and Wesker were sent in to steal his research data. Marcus was then dumped in the water, and the leech entered his body, consuming his brain and gaining his memories. The Queen Leech now sees itself as Marcus resurrected through divine work and seeks to use its powers to bring hell to the world.

The Queen Leech transforms into a giant leech, abandoning its humanoid appearance, and confronts Billy and Rebecca. They manage to escape up a cargo elevator that takes them back up to the plateau where the training school was located. They face off against the monster again in a large warehouse used for helicopter cargo transport. Realizing that the creature is sensitive to light, Rebecca manipulates the controls to the warehouse's retractable roof. Billy then fires at the creature with a magnum, causing it to fall down the elevator shaft just as the treatment plant explodes, along with the training school.

Rebecca and Billy escape out into the open. Looking out from the cliff-edge, Rebecca spots the mansion Enrico told her about and now knows where to go. Knowing Billy will have to be detained and sent for execution for murders he didn't commit, Rebecca takes his dog tag and declares him dead. He agrees to faking his death and walks out into the forest alone.