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The game starts in 2009, six years after the destruction of Umbrella. Chris Redfield has become a member of the Bioterrorism Security Assessment Alliance and is sent to investigate possible Bio Organic Weapon smuggling in Africa. Upon arriving in the Kijuju Autonomous Zone, Chris meets his partner, Sheva Alomar of the BSAA West African branch. Together, the two individuals attempt to rendezvous with the BSAA's "Alpha Team", who were attempting to intercept a supposed B.O.W smuggler named Ricardo Irving. However, the situation quickly escalates as their local contact is executed and the pair are forced to fight literal crowds of Plaga infested Majini .

Eventually, they find Captain DeChant, the only remaining member of Alpha Team. Fatally wounded, the Captain warns them of Irving's betrayal and gives them a file. Moments later, the two find themselves face-to-face with the Majini Uroborous Test Subject, seemingly made of leech-like worms. Destroying it, Chris and Sheva send the newly acquired data to HQ, soon meeting up with the West African BSAA Delta Team. Captain Josh Stone, leader of Delta team, gives Chris a memory card containing images of research material. Among these is an image of Chris's supposedly dead partner Jill Valentine. Chris and Sheva search for Irving, still determined to discover Jill's fate.

It is during this time that Chris reveals the truth behind Jill's supposed "Death": In 2006, Chris and Jill were working to track down Albert Wesker. They attempted to gain answers from Umbrella's former President, Oswell E. Spencer recently learning of his possible location. By the time they arrived at the estate, however, Wesker had already murdered Spencer, and they are forced to fight. Severely outmatching the pair, Wesker prepared to finish Chris off. Jill, sacrificing herself for Chris, tackled Wesker through the nearby window, and over the surrounding cliffs. Unable to find her body, the BSAA was forced to assume that both had died in the fall.

Chris and Sheva then encounter Irving, accompanied with a mysterious, cloaked woman, trying to get away. The BSAA catch up with Irving's boat. Then Irving has a flashback where the cloaked woman provides Irving with a Dominant Species Plaga. He uses it to try and defeat the BSAA agents. After defeat at the hands of Chris and Sheva, the dying Irving utters "Excella Gionne". With another possible lead, the pair trudge on.

When they come upon the pods seen in the research material, Chris frantically searches a nearby computer for Jill's location. They are forced to fight a huge B.O.W. named U-8 before they can check, and discover afterward that the pod is empty. Excella Gionne appears and denies any knowledge of Jill, much to Sheva's doubt. When Chris and Sheva encounter Excella again, they are fought off by the cloaked woman who accompanied Irving. A stray round knocks away her mask, and Wesker makes his appearance. The agitated Chris is quickly left speechless when Wesker reveals that the woman is Jill. Chris attempts to reason with her, but she attacks him with a flurry of hand to hand moves and starts an intense battle. Wesker arrogantly claims that he can spare only seven minutes for the pair, and eventually leaves Jill to handle them. Chris again calls out to Jill, and she attempts to resist the P30 used to control her. Wesker then activates a device, causing her great pain and administering more P30. Jill attacks Chris and Sheva again, and Chris and Sheva work together to remove the device from Jill's chest that is administering the P30. Chris then cradles the severely weakened Jill and she apologizes to both, stating that she was fully aware of her unintended actions. Ignoring her own state, Jill tells the pair to leave her and stop Wesker. Chris objects, but grudgingly agrees when Jill questions "Don't you trust your partner?" As they leave through an elevator, Jill finally says: "You're our only hope to survive this."

Chris and Sheva manage to board Wesker's ship and soon locate Excella. She flees, dropping a case of chemicals. After a brief flashback from Wesker's point of view, Chris and Sheva find the now dying Excella. Wesker then calls out over an intercom, casually discarding Excella. Simultaneously, Uroburos burst from her, killing her, and consuming the surrounding corpses. Destroying it, they discover that Wesker plans to spread Uroboros around the globe with a bomber. Jill then calls and informs them of Wesker's weakness: regular doses of a serum called PG67A/W. Overdoses would not maintain his superhuman abilities but weaken him, and Sheva realizes that the case Excella dropped contained the serum.

After doggedly pursuing Albert Wesker across the wilderness, Chris and Sheva find themselves in the bombers' hangar. Wesker had stocked the plane with enough Uroburos-carrying missiles to infect most of Earth. After combating Wesker in vain with conventional tactics, Chris resorts to injecting Wesker with the serums Excella dropped. This weakens him, allowing Chris and Sheva to fight on more level ground. Wesker is forced to escape with his Jet, but the BSAA team is able to pursue him. He reveals that the bomber is climbing to the ideal altitude for global infections. He is soon blasted out of an airlock by Chris, but manages to grab onto Sheva. Tortured by the memory of Jill, Chris jumps forward and catches her hand after she loses her grip. Sheva shoots Wesker in the face, and he falls into the caldera of an active volcano. The craft itself crashes into the same volcano shortly following.

The two agents are shocked to find a battered Wesker. Arrogant to the last, he plunges his right arm into an intact Uroboros missile, and is immediately engulfed by the symbiont. Chris and Sheva desperately fight the Uroburos-empowered Wesker precariously over a molten battlefield. The heaving volcano causes the ground to crack and melt, sending Wesker tumbling into the magma. Josh, piloting a BSAA helicopter, spots the pair, and Jill Valentine kicks a ladder to the them. Chris and Sheva barely escape as the ground melts beneath them.

Enraged and defiant, even in the face of his own mortality, Wesker attempts one last gambit, snagging the BSAA helicopter with his monstrously mutated arm. Jill tells Chris and Sheva to use the RPG-7s mounted in the rear of the rocking cabin. The two partners send a pair of anti-tank rockets racing down into the corrupted face of Albert Wesker, ending his life in a cloud of flame and ash.

As the chopper flies away in the final cutscene, Chris remarks: "More and more, I find myself wondering if it's all worth fighting for." He looks at Sheva and Jill and concludes with: "For a future without fear.....yeah, its worth it." The game ends with the chopper flying into the dawn.