The Umbrella Chronicles encompasses several scenarios, which are based on various plot elements from the Resident Evil series. The main characters include: Rebecca Chambers, Billy Coen, Chris Redfield, Jill Valentine, Carlos Oliveira, Albert Wesker, Ada Wong, Richard Aiken, and Hunk.

The first scenario, based on the events of Resident Evil Zero, follows STARS operative Rebecca Chambers, and former Marine Billy Coen as they venture through a train that eventually takes them to a derelict training facility. Once within the facility, they discover they are being stalked by James Marcus, one of the Umbrella Corporation's co-founders and former scientists, who has managed to resurrect himself with the aid of leech test-subjects. After a confrontation, Marcus mutates into a monstrosity, but is subdued by the duo. Chambers and Coen escape as the facility self-destructs. Another sub-chapter within the scenario traces Wesker's actions, now posing as the leader of STARS' Alpha team, as he attempts to escape the training facility. This chapter also introduces Sergei Vladimir and one of his bodyguard Tyrants, codenamed "IVAN".

The next scenario follows Chris Redfield and Jill Valentine, as opposed to the actual Resident Evil game, which features the two splitting up. Redfield and Valentine are forced to battle their way through a mansion full of undead residents before stumbling upon a secret Umbrella Corporation research facility in the mansion's basement. The two then discover the facility's most powerful creation, a Tyrant, and destroy it. The scenario features two different sub-chapters, which reveal Chambers' action between Resident Evil Zero and Resident Evil, as well as Wesker's reanimation and escape after his apparent death.

The next scenario visits Raccoon City during the events of Resident Evil 3: Nemesis. Valentine returns to the game, and is paired with mercenary Carlos Oliveira, as they attempt to survive an outbreak of the T-virus. After defeating several undead citizens, Valentine and Oliveira encounter Nemesis, an upgraded Tyrant, sent to kill Valentine.[16] They defeat Nemesis and escape Raccoon City before it is destroyed by the United States government in a desperate contingency measure. The scenario also features two sub-chapters, detailing Ada Wong and Hunk's background roles during the main scenario's events.

The game's final scenario is composed of new material, which trails Redfield and Valentine as they and other armed anti-bioweapon activists investigate the Umbrella Corporation's final stronghold in Russia. Now leading a group of armed activists, they storm the stronghold, encountering waves of undead soldiers and mutations. Despite their force sustaining heavy casualties, Redfield and Valentine enter the facility's inner sanctum, only to encounter and destroy the Umbrella Corporation's latest creation, the T-ALOS project. The game's final sub-chapter features Wesker infiltrating the facility in an attempt to recover the Umbrella Corporation's most important files. He is confronted by his long-time nemesis, Sergei Vladimir, whom he defeats. In the end, the Umbrella Corporation's secrets have finally been exposed. As a result, the U.S. government succeeds in its legal action against Umbrella's top officials.