(Covers information from Anderson's universe)
In an act to foil his lover, Alice, and her plans to expose Umbrella with Lisa Addison, Spence made his way into the virus chamber and stole several samples for the black market. He tossed a single container onto the ground as he exited the secure room a way to cover his tracks. The escaped virus quickly became airborne and traveled through the Hive's air conditioning system and made its way through the facility. The Red Queen, in an attempt to stop a disastrous viral outbreak, sealed off the offices in the facility and filled it with halon gas, suffocating everyone within. Elsewhere, the computer system flooded another chamber with water, drowning doctors Anna Bolt, Dr. Blue and Dr. Brown. Further attempts to kill the population resulted in elevator cables being cut and their safety devices rendered inert.
In her haste to stop the spread, the Red Queen did not notify the company as to the facility's situation, leading to an investigation. Some five hours after the attack, the specialist team arrived at the secondary entrance to the facility - a mansion in the nearby mountains. Inside they stumbled upon the recently awakened Alice, and Lisa's brother Matt, who had entered the mansion as part of his investigation.
With no where else to go, the three were taken down into the Hive with the squad. Initially, the team found no bodies at all, with the exception of Dr. Bolt and her team, still floating in what had become a water tank. Eventually, the team succeeded in disabling the Red Queen, loosing several of their members in the process - their leader and medic among them. This move, however, led to the release of all locks around the facility. Even worse, it would soon be revealed that the Red Queen had failed to exterminate the infected - the personnel were now zombies.
A surprise attack on the team would lead to more casualties, forcing the rest to escape through access ways. The team would realize that they would have to restore the Queen to bring order to chaos. She would reveal to them that they were all infected with the virus, and so she would not allow them to escape the facility. Meanwhile, Spence made his way to the transport terminal to go out alone, but was attacked by an escaped licker. Alice would head into the station and take Spence's suitcase from him, which contained samples of the anti-virus - evidently, Spence planned to sell these on the black market, too. Still not letting them go due to the hopelessness of Rain's case - the T-Virus had surpassed curable levels in her body, Alice attacked the AI before heading for the train with Rain and Matt.
Injecting themselves with the anti-virus, they were then attacked by the Licker which, before its death, infected Matt with a mutant strain of the virus. Rain would die and resurrect as the Red Queen expected. Making it to the mansion, Alice and Matt would be confronted by a team of Umbrella scientists, who would strap the two to stretchers for immediate biological study, with Matt being placed on the "Nemesis program". Their next order of business: the reopening of the Hive.