September 28, 1998. Racoon City is on its last legs. The city has been overrun by a horde of zombies, the products of a mysterious plague that has overtaken the city. Chaos has broken out, and the few survivors are either running for their lives or cowering in their personal shelters, waiting for the nightmare to end.
For the most part, however, this goes unnoticed by former S.T.A.R.S. Officer Jill Valentine. Placed under house arrest after refusing to be silent over the Umbrella Corporation's involvement in the Spencer Mansion Incident (in no small part because police chief Brian Irons happened to be in Umbrella's pocket), Jill has been attempting to unravel Umbrella's conspiracy, despite the horrible nightmares she has been having. Her investigation is put to a halt, however, when she receives a phone call from her former teammate Brad 'Chickenheart' Vickers, instructing her to leave the city immediately. Before she can offer a reply, a huge figure clad in a strange black attire bursts through the wall, knocking Jill to the ground. The figure ferociously manhandles to former officer, shrugging off headshots as it attempts to kill her. Jill manages to escape into the hallway, but the figure continues to chase her through the building, at one point revealing a fleshy tentacle that it attempts to capture her with.
Eventually exiting the building, and with her pursuer apparently crushed by the collapsing structure, Jill links up with Brad as a helicopter flies overhead, searching for survivors. Attempting to flag down the aircraft, the two come upon a horde of zombies - just like the ones at the Spencer Mansion. The horde manages to tear down a police barrier, and although the pair manage to make it inside a nearby building, Brad is bitten by a zombie while trying to blockade the doors. Aware that he will likely not survive the night, Vickers urges Jill to save herself, and she reluctantly complies. Managing to successfully flag down the helicopter, Jill is forced to fight through a small horde of undead to reach a nearby park structure for pickup. The black clad entity that pursued her earlier destroys the aircraft, however, and continues to try and kill Jill. The fight is briefly interrupted when Jill rams a car into the creature, knocking both of them off the roof. Jill struggles to crawl away from the wreck as the monster stands up and resumes pursuit, barely even flinching as the car explodes, revealing its hideous, stitched-together face.
This is Nemesis, an Umbrella T-103 Tyrant bonded with an NE-α parasite, tasked with eliminating the S.T.A.R.S.
Salvation comes in the form of a heavily armed Hispanic man, who fires a quad barrel rocket launcher at the tyrant. Nemesis is able to catch and redirect the first rocket with his tentacle, but the second one incapacitates the Pursuer. Having expended the first two rockets prior to encountering Jill, the soldier discards his weapon and helps Jill to her feet, before leading her to safety and introducing himself as Carlos Oliveira of the Umbrella Biohazard Countermeasure Service, U.B.C.S. for short. Jill is less than pleased, well aware that Umbrella has a hand in the disaster going on right now, though Carlos believes she is wrong. Nonetheless, he takes her to a subway car where his platoon leader, Mikhail Victor, has gathered some of the remaining civilians and is attempting to evacuate them from the city. Victor recognizes Jill and chides Carlos for not even thinking to ask her name.
Despite her misgivings toward Umbrella, Jill agrees to help the U.B.C.S. complete their mission, if only for the sake of the civilians they have rescued. Carlos informs her that she will need to reactivate the nearby power station before the train can be started up again. After extinguishing a fire preventing her from entering the building, she encounters one of Carlos' squad-mates, the injured Murphy Seeker. Before she can help him, however, he is executed by another U.B.C.S. soldier, Nikolai Ginovaef. Jill lambasts him for his callousness, only for Nikolai to mock her 'bleeding heart', insisting that Murphy was infected and that Jill's sense of compassion will only get her killed. Disturbed by Nikolai's brutality, Jill continues on her way.
In the heart of the station, Jill finds a strange, cocoon-like nest. She is then ambushed and impregnated by a spider like creature known as a Drain Deimos, but thanks to a note she had found earlier, Jill manages to kill the gestating larva. Fighting off a small horde of the creatures, Jill is able to reset all of breakers and restore power to the area, destroying the nest and killing the mutants in the process.
As Jill returns to the subway station, Nemesis reveals that it had survived its previous encounter with Jill and Carlos, and resumes its efforts to kill her. Despite Carlos' pleas, Jill refuses to return until after she has gotten subway traffic control reactivated. Despite the efforts of Nemesis and the other zombies, several of which have been parasitized by the NE-α's spawn, Jill accomplishes her mission and links up with Carlos. Joining them are Nikolai and another U.B.C.S. member, Tyrell Patrick. Nikolai notes that it will be impossible to fight their way out of the city with all of the T-virus zombies surrounding them, then throws another insult at Jill, telling Oliveira that she is unreliable and will be the death of him. Nemesis manages to break his way into the station, leading Jill to break off from the rest of the group in an effort to lure him away.
Jill's attempt at playing decoy lead her to the sewers, where she attempts to contact Carlos, only to find that she is too far underground to get a signal, forcing her to search for a route to the surface. Along the way, she encounters strange, salamander-like bipedal creatures, which she learns are a variant of the Hunter Series she encountered in the Spencer Mansion - Hunter Gammas, to be specific. Slated for destruction due to their inability to function outside of wet environments, they were instead released into the sewers by Dr. Logan Carlisle while he attempted to negotiate their sale to Umbrella Europe. Eventually managing to regain contact with Carlos, she is informed that they will depart once she has returned.
As Jill climbs out of the sewers, however, she is greeted once again by Nemesis, who has acquired a flamethrower. Tossing Jill aside, the tyrant refuses to kill her immediately - he wants her to fight back. Jill decides instead to retreat, making her way into a nearby construction, Nemesis in pursuit all the while. When the B.O.W. corners her atop the roof, she engages him in battle, eventually defeating him by destroying the weapon's fuel tank and subjecting him to a veritable hail of gunfire. Informing Carlos that the creature is "dead", Jill makes her way back to the station, cutting through Kendo's Gun Shop to save time. She is briefly surprised by Robert Kendo, though the situation is quickly sorted out. Jill offers to take Kendo to the station with her, but he declines.
Nemesis soon reveals that he survived the rooftop battle, and now has access to a laser-guided rocket launcher. Jill evades the B.O.W. and his explosives until she reaches the station, where Carlos appears to kill the tyrant by blowing up a fuel tanker while the creature is standing right next to it. Rejoining the rest of the U.B.C.S., Carlos is told that he and Tyrell have new orders - find Dr. Nathaniel Bard, who is developing a vaccine for the T-Virus that could save the city. Jill boards the train and is praised by Nikolai, who claims that she is learning that the only thing that matters is her life. The subway train soon departs.
On September 29, at 2:11 AM, Nikolai remarks that he is skeptical over whether or not Bard is still alive. Mikhail shuts down his concerns, before revealing he believes that Nikolai may have ulterior motivations. Nikolai merely chuckles in response, but any further conversation is interrupted when Nemesis reappears, tearing into the civilian car and killing all of its occupants. Mikhail instructs Jill to retreat into the next car while he holds off the pursuer, only for Nikolai to lock both Jill and Mikhail in with the Tyrant. When questioned, he stuns Valentine by revealing that he is aware that Nemesis is only after Jill. Mortally wounded by the monster, Mikhail detonates a pack of C4, causing the train to derail, and knocking Jill unconscious.
Twenty three minutes later, Tyrell and Carlos arrive at the RPD, witnessing Lieutenant Marvin Branagh being bitten by the zombified Brad. After killing the zombie, the two begin searching for Bard, who their intel suggests is in the S.T.A.R.S. office. Carlos is forced to fight his way through zombies and, surprisingly, Lickers to reach the office, where he contacts Dr. Bard - the latter having escaped the office only to now find himself trapped in a hospital. He reveals that Umbrella is hunting its employees so that they cannot incriminate the corporation over its shady dealings. Tyrell then tries to use the computer to trace Dr. Bard's location while Carlos receives a call from Jill, who informs them about the train derailing and Nikolai leaving them to die. When Jill suddenly stops speaking, Carlos rushes over to find her, while Tyrell continues trying to locate Bard.
Several minutes earlier, Jill had regained consciousness and, realizing she was the only survivor of the crash, attempted to contact Carlos, only to find she was out of range. She makes her way to Saint Michael's Clock Tower Plaza, where she witnesses a burning Nemesis fall into the river before contacting Carlos to fill him in on recent events. Said call is interrupted when Nemesis bursts out of the river, now heavily mutated into a creature resembling a xenomorph. After a brief chase across the bridge, Jill is once again forced to battle the creature, eventually defeating him with a grenade launcher. As she attempts to escape through the clock tower, though, Nemesis regains consciousness and grabs her with his left arm. Jill manages to shoot the lock on the overhanging portcullis, which severs Nemesis' arm as it falls. However, the tyrant swiftly grows a new, tentacled arm, which it uses to impale Jill with a bone spike, infecting her with the T-Virus. Both then pass out from their wounds. Nikolai then arrives on the scene and "thanks" Jill for her help, revealing himself to be an Umbrella supervisor recording the carnage in the city for the Umbrella board of directors.
Half a day later, Carlos finds Jill and decides to take her to Spencer Memorial Hospital, where Tyrell has determined Bard to be hiding. Nemesis is nowhere to be seen, implying the tyrant has healed himself and begun searching for the remaining S.T.A.R.S. members, unaware all surviving members have already left the city. Carlos manages to carry Jill to the hospital at 9:20 PM that night. After ensuring she is safe, he goes out to find Bard and, hopefully, the vaccine. Oh his way, he encounters not only zombies, but also hulking humanoid creatures with a mixture of reptilian and insectoid traits. Unknown to him, these are another strain of the Hunter-Series: the Hunter-Beta.
Eventually, sometime past midnight, September 30th, Carlos reaches Bard's office, only to find the doctor dead - shot by Nikolai, though Carlos doesn't know this. Carlos then watches a video Bard made at 11pm the previous day (literally the hour prior), where he reveals that Jill was correct - Umbrella caused the Raccoon City Outbreak by releasing T-Virus samples into the city (albeit accidentally due to complications with the capture of Dr. William Birkin, detailed in the events of the previous game). Shocked to learn that Jill was correct, Carlos is amazed that she was still willing to trust him despite his affiliation with Umbrella. Acquiring a vaccine sample from a nearby freezer, Carlos rushes back to the hospital to administer it to Jill. A short while later, Tyrell arrives and turns on one of the televisions, where it is revealed that the US Military plans to nuke Raccoon City on October 1st, 1998 to stop the outbreak (and also, secretly, to cover up their dealings with Umbrella). A massive horde of zombies, alongside several Hunter Betas, assaults the hospital, though Carlos manages to stem the tide and eventually halt their advance by using C4 to demolish a pillar to cover the entrance. He then asks Tyrell to watch over Jill and attempt to convince the military to postpone the bombing while he searches for the rest of the cure that Dr. Bard manufactured, which is now stored in an underground facility.
After one additional nightmare, Jill awakens three minutes after midnight on October 1st, 1998, mere hours before the city is to be destroyed. She finds Tyrell trying to contact someone with the authority to postpone the missile strike until Carlos can return from underground with the cure. Tyrell fills Jill in on what is going on, after which Jill heads underground. Her search comes to a halt when she finds Nikolai, who she attempts to pursue, but he eventually evades her. Returning to the surface, Jill regroups with Tyrell, who informs her that he was able to arrange for the bombing to be scrubbed if a sample of the cure can be provided to the military. Before they can go anywhere, Nemesis returns and kills Tyrell. After managing to escape the pursuer once again, Jill makes her way into the underground NEST-2 facility, where she is able to synthesize a vaccine.
Nemesis attempts to slay Jill yet again, but the former S.T.A.R.S. member cheats death once again, after which she makes her way to the Disposal Room. The pursuer bursts through a door and tackles her, causing her to fall onto a platform and lose the cure. Nikolai takes the cure and, after offering to give it back if she puts on a good show fighting Nemesis, drops Jill into the disposal bay to battle Nemesis, with the added danger of a horde of zombies. Carlos then appears, and assists Jill by calling out Nemesis' location when the tyrant tires to hide behind the acid tanks in the area. After the beast falls yet again, Carlos rams a crane arm into it, then pulls Jill out while flooding the arena with acid, apparently killing Nemesis.
Jill and Carlos manage to catch up with Nikolai, only for a huge cocoon to make its way into the room and explode, revealing the final form of Nemesis, now mutated almost beyond recognition. Ordering Carlos to pursue Nikolai, Jill engages in a final battle with Nemesis, using a prototype weapon called the Ferromagnetic Infantry-use Next Generation Railgun, also known as the FINGeR. After being forced to realign its cooling system when the cores that power it come loose, Jill manages to cripple Nemesis to the point it collapses, after which she shoves the FINGeR down his throat and fires a third and final time, completely obliterating the central part of the tyrant and finally killing it.
Making her way to the roof, Jill finds Carlos unconscious, at which point Nikolai attacks and disarms her. He then tosses her the vaccine canister as promised, only to shoot it, condemning the city to die out of spite for Jill. She asks him if he has any idea what he has done, only for Nikolai to reveal that he doesn't care - his client wants Umbrella reduced to rubble. Before Nikolai can kill Jill, Carlos tackles him and the two engage in a fight, ending with Carlos pulling Nikolai into a choke hold and ordering Jill to shoot. After a moment of hesitation due to the possibility of hitting Carlos, she complies and shoots Nikolai in the shoulder. Jill questions Nikolai again as to why he destroyed the vaccine, and when he answers cryptically, she questions him about who his employer is. When Nikolai attempts to use the identity of his employer as a bargaining chip to be taken to safety, however, Jill and Carlos both decide to leave him. The former rebutes Nikolai's warning that she will never learn the truth if he dies by stating she doesn't mind a little detective work, after which both Oliveira and Valentine board the helicopter parked on the roof, leaving Nikolai to die.
An indeterminate time later, Jill witnesses the missile fired by the government arrive and destroy Raccoon City, the shockwave briefly throwing the helicopter off course. Jill monologues over how it was not monsters that destroyed the city, but human greed, and resolves to make sure that the city's ashes would be Umbrella's ashes as well.
After the credits roll, an unknown individual grabs the broken vaccine canister and departs to locations unknown.
