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Beginnings starts with Albert Wesker and William Birkin in the surveillance room seen in Resident Evil Zero. Birkin and Wesker realize that they can't contain the inevitable biohazard caused by the newly resurrected James Marcus. Wesker decides to abandon Umbrella before it inevitable collapses. Birkin objects, as he's still working on the more powerful G-virus. Wesker explains his plans to Birkin of luring the S.T.A.R.S. Alpha team into the Spencer Mansion to gather combat data for the B.O.W.s before leaving. Birkin then decides to set off the self-destruct system to blow up the Executive Training Facility.
Wesker begins in the Umbrella Factory, near the cable car. The power is out, so he needs to restore it to use the cable car. Wesker fights his way to the turntable and rides it down to the Underground Laboratory. Wesker then proceeds to the Umbrella Waste Disposal Facility, where he turns on the power. He then backtracks to the turntable, and rides it back up to the factory. While on the lift, the Tyrant fought previously by Rebecca and Billy leaps down onto the turntable to engage Wesker in battle. Though Wesker defeats it, once the lift has reached the factory, the Tyrant recovers. Wesker fights it one last time before it dies for good. Wesker returns to the cable car station, now supplied with power, and rides it to the Executive Training Facility.
Wesker begins the second half of Beginnings outside the Training Facility, near the church. Wesker then proceeds to fight his way through the facility to the main hall, where he enters the underground and the area where the Ecliptic Express crashed. In this room, Wesker is confronted by Sergei Vladimir. Sergei reprimands Wesker for attempting to leave without reclaiming the facility or taking responsibility for his "failure". When Wesker responds that the facility's destruction will dispose of the virus, Sergei reminds him that he is not in charge. Sergei then sets one of his Ivan bodyguards loose on Wesker to teach him a "lesson". Wesker emerges victorious over the Tyrant, and the conflict is brought to a halt as the upper levels of the facility explode, sending a brief rush of flame across the room. Wesker takes his opportunity to escape and rally the S.T.A.R.S. members for their mission to the Arklay Mansion, while Sergei also leaves for the mansion to retrieve T.A.L.O.S. and the U.M.F.-013.
Although the chapter elaborates on the events after Wesker proceeds to leave his duty at the Umbrella Executive Training Center, it does have some differences from Resident Evil Zero:
- Wesker and Birkin were apparently still in the monitor room within the Underground Lab in the scenario, while in Resident Evil Zero, they had actually been at the Turntable elevator area, with the former boarding the elevator.
- Marcus is not actually mentioned at all, and the way the scene was framed made it seem as though they realized Umbrella was finished due to Rebecca and Billy traversing through the mansion.
- Birkin was shown to be a lot more angry at Wesker leaving Umbrella than in Zero.