(Capcom's primary storyline)
During the Raccoon City Destruction Incident, Nielsen was ordered by the corporation to remain in the city and conduct an operation to reclaim cargo stolen from his dock. Worried about the incriminating nature B.O.W.s recovered from an Umbrella dock, Nielson was charged with the elimination of the thief, Captain Rodriguez, and anyone seen helping him including women and children.
On October 1, Nielsen took command of Arnold's UBCS team and had them plant landmines in the streets around Rodriguez' helicopter, while a missile launcher was delivered by truck to a warehouse building to be used as their base of operations.
- If the player fails to escape by helicopter, Tommy will attempt to shoot it down, inadvertently releasing Nyx. In that scenario, his entire UBCS team is killed by the B.O.W. but Tommy's fate is not revealed.