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"Jill Valentine is one of the last remaining people in Raccoon City to witness the atrocities Umbrella performed. To stop her, Umbrella unleashes their ultimate secret weapon; Nemesis!"
— PlayStation Store description
"A series of strange disappearances have been occurring in the American Midwest within a place called Raccoon City. A specialist squad of the police force known as S.T.A.R.S. has been investigating the case, and have determined that the pharmaceutical company Umbrella and their biological weapon, the T-Virus, are behind the incidents—though they've lost several members in the process. Jill Valentine and the other surviving S.T.A.R.S. members try to make this truth known, but find that the police department itself is under Umbrella's sway and their reports are rejected out of hand.

However, soon reports of a grisly "cannibal virus" begin to surface, and vicious dogs begin roaming the streets. With the viral plague spreading through the town and to her very doorstep, Jill is determined to survive.
However, unbeknownst to Jill, an extremely powerful pursuer has already been dispatched to eliminate her.
— Official Website

The story begins with the live-action/CGI opening cutscene of news reports flooding in about the outbreak in Raccoon City, while Umbrella scientists finish work on their latest project: The Nemesis. After the opening title sequence, the pod containing the Nemesis within can be seen being loaded onto a chopper.

Afterward, Jill Valentine experiences a nightmare, where she closes her window and stumbles into her bathroom. She shuts off the faucet of the sink, only to see blood patter into the sink. When she looks up, she sees herself beginning to transform, and recoils in terror, retreating into the darkness. When she reemerges into the light, she sees she has physically transformed into a zombie. Knowing she has little time left, she picks up a nearby handgun and presses the barrel to her temple. She then fires, before waking up.

The game sets on September 28th, 8:07 PM. Jill reawakens, having slept while doing investigations on Umbrella from her apartment, and receives a frantic phone call from Brad Vickers. He warns her she has to leave, before being abruptly cut off by the Nemesis bursting through the wall. She narrowly manages to escape its clutches by dashing into the hallway and another apartment, then reaching the fire escape. Going down, she briefly absorbs the carnage Raccoon has fallen into before reentering the apartment building. Jill is once again ambushed by the Nemesis and is nearly caught, once by its tentacle, moments later by it attempting to use the debris of the building to pin her, before she escapes.

Jill encounters Brad, who explains that, while he doesn't know what the creature is, he is aware it is after the S.T.A.R.S. members who are in Raccoon City. Zombies break down nearby barricades, and the pair has to retreat inside a bar, but zombies manage to break in and one of them bites Brad, who realizes that there's no time and tells Jill she must escape and that she mustn't screw up like he did. She leaves him to hold off the zombies, vouching to rendezvous with a helicopter atop the parking garage building. Making her way into a storage room, she encounters Dario Rosso, who locks himself inside a storage container, and she fails to convince him to escape with her.

Arriving in the parking garage, she makes her way past several zombies and takes an elevator up to the roof, where the helicopter awaits. The chopper blows up, and Nemesis emerges from the shadows. She uses a car to ram into the creature and they fall off the building, Jill manages to crawl out of the wreckage before the car explodes and burns away the Nemesis' face mask, allowing her to finally see her pursuer for what it truly is. She is saved by Carlos Oliveira, who uses an anti-tank rocket launcher to briefly incapacitate Nemesis, and he takes her to a subway station on Redstone street for shelter as Nemesis falls to its knees.

Carlos then tells her that he is a part of Umbrella Biohazard Countermeasure Service or U.B.C.S. for short. After hearing this, Jill lashes out at Carlos saying that Umbrella was the one who cause all of this. But having left with no choice, she decides to go with him. He then introduces her to Captain and platoon leader Mikhail Viktor, who asks her for help in evacuating some survivors via the subway train, Jill reluctantly agrees, but only because she wishes to save the civilians and not the U.B.C.S. members. Carlos then hands her a radio, informing her that they should stay in touch, while also nicknaming her "Supercop".

Jill reaches the topside of Raccoon city streets and is instructed by Carlos to head for the substation, and once she reaches the main road, he then tells her to go through the alley, but she discovers it has been set ablaze. She then traverses the streets and alleys to acquire a fire hose, and puts out the fire by attaching the fire hose to a nearby fire hydrant. Once inside the building, she finds an injured Murphy Seeker, but before she can treat him, Nikolai Zinoviev appears from behind and shoots Murphy in the head. Shocked and outraged, she angrily tells him that he might not have been infected, but he retaliates by taunting her, saying that all of the S.T.A.R.S members are soft and suggest she to go back for the subway station, as they don't need "a bleeding heart like her" getting in the way.

Jill then proceeds onward and notices a cocoon-like nest is laying on top of the cables. Jill is then ambushed by a hive of Drain Deimos, being forcefully impregnated by one, but she succeeds in killing the unborn larva and resetting the circuit breakers, which restores the power at the substation and to the metropolitan area, destroying the nest in the process.

Upon returning, Jill is tracked down by Nemesis again, and after narrowly avoiding it, informs Carlos that Nemesis is still alive. Carlos tells her to come back to the station, but she refuses to return until she gets traffic control online again. Finally reaching her destination, Carlos instructs her to plot out a route from Redstone street to Fox Park Station, Jill accomplishes this task and heads back to the station.

Jill then meets up with Carlos. Nikolai and Tyrell Patrick appear, and Nikolai informs them that there is no chance of fighting their way out of the city as it is filled with T-infected creatures. Nikolai notices Jill and again taunts her, telling Carlos that she is unreliable and will get him killed. Nemesis then storms into the station, so Jill shuts the gate and decides to use herself as bait to draw him away and hopefully buy them some time. She then lures it away and escapes through a ventilation duct to the sewers.

Attempting to contact Carlos, she gets no signal and chooses to head for the surface. She navigates through the sewers to get into the city above, and upon exploring, she encounters numerous Hunter Gammas that were smuggled into Raccoon by Umbrella scientist Doctor Logan Carlisle, who refused Umbrella's order to destroy the failed bioweapons and attempted to sell them to Umbrella Europe. Jill manages to reach the top, and contacts Carlos again, who is relieved to hear that she is alive and informs her that they will leave once she gets back.

She attempts to reach to street level only to realize that she was tracked again by the relentless Nemesis, who grabs her by the head and tosses her outside. It then proceeds to chase her with its brand-new flamethrower, forcing her to evade its attacks by ascending the building she is in. Escaping to the rooftop, she is forced to duel with the Nemesis, destroying its fuel tank and ultimately incapacitating it. Believing she killed it, Jill radio Carlos informs him that it is "dead", she then cuts through Kendo's gun shop to reach the station. When she enters, she is jumped by a gun-wielding Robert Kendo, but she is relieved to see that he is alright and suggests that he comes with her to the station but he refuses, reassuring her that he will be alright and bids her goodbye.

Soon after, she is attacked by Nemesis, now wielding a rocket launcher with a laser guiding system, and it continues in its pursuit of her. Carlos radios again telling her he knows how to slow it down, but she has to lead it back to the station, Nemesis attempts a variety of ways to terminate its target, but is halted when Jill reaches the safety of the subway station, but not before Carlos shoots a gasoline truck that explodes on the B.O.W. They move to the station and meet up with other U.B.C.S. members. Mikhail praised Jill for her actions and tells her to get on the train. Meanwhile, the captain orders Carlos and Tyrell to head back to the city and find Dr. Nathaniel Bard, whose vaccine research could save the city. Nikolai, waiting inside the train, praises her, saying that she is learning that all that matters is her own life. Mikhail enters and they start their escape from the doomed city.

On September 29th, at 2:11 AM, Nikolai asks Mikhail if he thinks that Dr. Bard could be alive, but Mikhail rebuffs him with suspicions that Nikolai has ulterior motives and voices his concerns. Nikolai only responds with a chuckle before Nemesis storms onto the train, killing all of the civilians that took the shelter inside the train. Outraged by this, Jill attempts to attack it, but Mikhail stops her and instructs her to get to the back of the train, but Nikolai locks the door, trapping Jill and injured Mikhail with the assailant. Nemesis then pierces and ensnare Mikhail with a tentacle, but Mikhail already uses a C4 detonator in a final sacrifice to try to destroy the Tyrant, separating them from the subway car Jill is in. Her car begins derailing, and she flies into the wall of the train, with the impact from the hit knocking Jill unconscious.

23 minutes later, Carlos and Tyrell arrive at the RPD, to the makeshift cemetery. On their way, they witness Lieutenant Marvin Branagh getting bitten by a zombified Brad. Marvin then runs back to the station, locking the front door. Killing the zombie, they enter the RPD and search for Dr. Bard, who is, according to the intel Mikhail received, is inside the S.T.A.R.S. office. On his way, Carlos encounters the lickers and zombies that have overrun the station, but manages to reach the office and contacts Bard, who reveals that he escaped and is now trapped at the hospital that is filled with B.O.W.s and zombies. Bard reveals that Umbrella is killing all the researchers, for they are the witnesses that might incriminate Umbrella by revealing their illegal activities and its connection to the outbreak. He urges them to get him out before ending the call. Tyrell then hacks the computer and tries to trace Bard's location as Carlos receives a transmission from Jill, who informs him that everyone on the train is dead and that Nikolai left them to die before abruptly ending the call. Carlos then rushes to Jill's location while Tyrell remains to track Bard at 4:43 AM.

Several minutes earlier, Jill crawled out of the subway car, realizing that she is the only one to survive the train derailment, so she tries to contact Carlos but is out of range; she manages to reach the city park near the Saint Michael's Clock Tower Plaza and hears the roaring pain of Nemesis. Jill crosses the walkway bridge where she sees a burning Nemesis tumble his way down the riverbank, and she contacts Carlos afterwards and informs him of what has transpired after he left. In the nidst of the call, she was attacked by mutated Nemesis, who emerges from the river, where it had lost the makeshift coat it had, having mutated into a quadrupedal, ferocious canine-like creature with huge claws. Jill runs from it until she is cornered in the plaza, and is forced to fight. Jill knocks the creature out with the explosive rounds after a long duel, but before she can leave the area, Nemesis attacks her again, grabbing her by the feet until she shoots the chain that is holding the metal portcullis. The portcullis falls and amputates the arm of the Nemesis, but it regrows the arm in the form of a tentacle, and it manages to attack and infect her by impaling her arm with a bone spike, before they both fall to the ground, losing consciousness. Nikolai appears smiling and thanks her for doing him a big favor.

Half a day later, Carlos finds Jill and carries her to the Spencer Memorial Hospital hoping Bard could cure her, he radios Tyrell telling that they would meet there. On September 29th, 9:20 PM, Carlos manages to reach the hospital and puts Jill down on the bed in the Makeshift Sickroom, he then goes out and searches for the vaccine. Carlos finds the office of Dr. Nathaniel Bard, to enter it he finds a tape player and the audiotape with Bard's voice. On the tape, a young nurse asked what the documents were doing in his office in the first place but Bard answers this with his delusional grandeur, insults towards her career, ruthlessly taunts her to go back to wipe the patients' asses and orders her to go polish his shoes. Carlos enters the office and finds Bard dead with a gunshot wound to the head, having been assassinated by Nikolai, although it is not known to Carlos, he finds a computer that contains a video recording dated back to September 29th, 11 PM, in the video, Bard reveals that all of Raccoon City's suffering began with the release of a biological weapon known as the T-Virus, his employer Umbrella engineered the virus and ordered their team to develop a vaccine, he explained that he had one sample of the vaccine in his office while the rest of it is was stored in an underground facility; the executives on the board wanted to destroy the vaccine in an effort to erase any evidence the virus has ever existed, the record ended when he heard a sound just right outside of the room. Shocked by this revelation, Carlos is surprised that Jill still trusted him despite knowing the truth about Umbrella. Obtaining the vaccine he rushes back to Makeshift room and uses the vaccine on Jill, Tyrell arrives at the hospital sometime later and turns on the TV to reveal an announcement with the date of September 30th that the contagion is uncontainable and in October 1st, US government will launch a missile strike, eradicating the virus along with the city, they urge the survivors who are still alive to get out of the city before the deadline. The zombies surround the hospital, Carlos then goes outside to fend off the creatures to protect Jill to give Tyrell enough time to hack into the hospital's security to shut the doors down. The hordes of zombies storm in through the front door, Carlos uses a C4 detonator to knock down a pillar covering the front entrance, he then goes back to the room and tells Tyrell to contact someone in the government to stall the missile strike while he searches for the cure.

Jill awakens to find Carlos, who tells her that the city is now safe and its finally over, suddenly he coughs up blood and nearly turns to a zombie, he begs for her to pull the trigger as it is the only way but finds herself unable to. A now zombified Carlos lunges at her and eats her. Jill wakes up again from a nightmare, she finds that her wound is treated and turns her attention towards the TV, the date is now October 1st, 12:03 AM, just hours away from the missile strike. She finds Tyrell outside still trying to get a hold of someone with any clearance to stop the missile strike and informs her that Carlos is underground trying to get the stocks of vaccine, enough to give the city some hope, she then goes after Carlos. Jill finds a secret complex that leads her to an underground facility, she finds an observant Nikolai, She pursues him only to find Nikolai had run away. She regroups with Tyrell, who got through to the government that they are willing to call off the strike if they deliver the vaccine to them, they then move forward only to get ambushed by the mutated Nemesis again, the creature incapacitates Tyrell before it impales him with its tentacles, Tyrell urges for Jill to go on, Nemesis then tosses his lifeless body, she makes a run for it and manages to shut the door behind them; Jill enters NEST2 facility, navigates through the building and is successful in vaccine synthesis, only to be ambushed by Nemesis.

After escaping the ferocious pursuer, Jill arrives at the Disposal Center, Nemesis follows her and breaks in but falls, Jill barely manages to grab on some ledges and drops the vaccine, Nikolai then appears and wants to make a deal that she goes down there fights the Nemesis while he will record the battle and obtain battle data which he will sell and gain profit, in return, she will be given back her vaccine. He then sends her down, where she battles the Nemesis. Carlos appears and assists her during the fight, After badly injuring Nemesis with weapons and also with the crane, he then drops the crane for Jill but as she climbs on it, Nemesis attempts to attack her again, only to get hit by the crane operated by Carlos, who then floods the center of the area with potent solvents from the tanks, dissolving Nemesis into a bloody pulp in the process.

Carlos then drops Jill and tells her that he will meet her up ahead, she pursues Nikolai, pointing her gun at him demanding him to give her the vaccine but he refuses. During this heated moment, Nemesis burst into the room as a giant blob, Nikolai says that data on this can be worth millions and bids her good luck before running off. Carlos appears and Jill tells him to go after him while she will deal with Nemesis one last time, he complies and runs after Nikolai to the roof of the building. Jill then opens the compartment contains a Ferromagnetic Infantry-use Next Generation Railgun or also known as its acronym, FINGeR, she fires the powerful weapon at the Nemesis. After Nemesis is injured, she shoves the railgun to Nemesis's mouth and fires one last shot that completely obliterates the creature.

Jill resumes her pursuit of Nikolai. On the roof, she finds Carlos knocked unconscious, Nikolai then attacks and knocks Jill's gun out of her hand, he tosses her the vaccine canister only to shoot it, thus dooming the city. Outraged by this, she asks him if he has any idea what he had just done but he only responds that he doesn't care, as his client asks him to reduce Umbrella to rubble. Nikolai prepares to kill Jill until Carlos tackles him and the two engages in combat, Carlos then puts Nikolai in a chokehold and shouts for Jill to shoot him, she is reluctant at first for fear of the bullet hitting Carlos, but finally complies and shoots Nikolai in the shoulder. She rushes to Carlos's aid, he tells her that he couldn't just leave her in a world without him for that will be too cruel. Jill then again asks an injured Nikolai why he had destroyed the vaccine, he responds cryptically and she asks him who he was working for but instead of an answer, he pleads that he would tell and pay if she gets him out of here, Jill decides to leave him on the roof but not before Nikolai warns her that if he dies then she will never find out the truth but Jill responds that she doesn't mind a little detective work and so Carlos and Jill board the helicopter, seemingly leaving Nikolai to die with the city.

Sometime later, they are in the outskirt of the city as Jill witness a missile fired by the Government, Raccoon City is destroyed with a Thermobaric Bomb. the shockwave disrupts the helicopter's trajectory. Now alone with her thoughts as Carlos rests, she feels empty and cold as the shockwave washed over them, and feels that all of the deaths and all the tragedy could have been prevented if it weren't for greed, human greed. she decides that her city's ashes would be Umbrella's ashes as well.

The post-credit scene shows an unknown person grabbing the broken vaccine canister off a desk, making off with it.

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