(Covers information from Anderson's universe)
Following her escape from the Hive, Alice was taken into Umbrella's custody and experimented on in the bowels of the Raccoon City Hospital. During the experiments, she was deliberately infected with the t-virus, and something unexpected happened. Alice's DNA bonded with the virus on a cellular level, adapting to it and changing it. Resulting in her strength and speed being increased. With Alice's DNA bonding and also escaping from Umbrella, Alice had to stay low. Umbrella already had her blood samples and were trying to clone her and always resulted badly.
Following the outbreak of the T-virus in Raccoon City, Major Timothy Cain brought both Alice and Matt Addison, now known as "Nemesis", out of their sleep, in the hopes that the two would confront one another. They did, in fact, meet and their first fight ended in a stalemate when both combatants retreated.
Shortly before dawn, when the city was scheduled to be sterilized via airstrike, the two experiments met and fought once again. Alice's proved herself the victor, but refused to join with Umbrella and escaped on a helicopter, which later crashed in the nearby Arklay Mountains, apparently killing her.
Her body was taken by Isaacs to a facility in Detroit, where she was revived and further operated on. She escaped, however, and demonstrated remarkable powers both physical and psionic, demonstrating the ability to kill a man just by thinking it. Afterwards, Umbrella struggled in vain to track her, a task made difficult by Alice's efforts to remain hidden and off the radar.
Escalation and Aftermath
After the worldwide pandemic turned most of the population into zombies, Dr. Isaacs continued Program Alice via cloning, trying to perfect a way to neutralize the Undead. Eventually, his research hit a wall, and it became necessary to find the original Alice.
All the while, her telekinetic abilities were growing. She was able to control an explosion and use it to wipe out a swarm of crows. However, any time she used these remarkable powers, the energy was detectable by the White Queen's sensors, enabling Umbrella to track her movement. In the end, Alice confronted and killed Isaacs; the program was considered a failure and closed by Albert Wesker.
Though the program was officially closed by Wesker, the head of Umbrella appeared to make the declaration final when he robbed Alice of her t-virus abilities with a serum that destroyed the t-cells in her system; Alice was rendered "human", forced to fall back on her skills learned as an operative. However, he later restored Alice's powers, her strength needed to fight the Red Queen and the Umbrella Corporation.