ANo, Alice did not die and that was not a clone. When Alice died, Umbrella injected her with more of the T-Virus, bringing her back to life with telekinetic powers. They say that she was the actual Alice and, in Resident Evil: Extinction, they confirm that Alice is the original Alice and that they did not start the clones until Extinction.
AThere were some newspaper clippings in Jill Valentine's apartment that said "STARS operative Jill Valentine and others are on temporary suspension after a mission in the Arklay Mountains", which implies that the Mansion Incident in the first game did happen in the movie universe but was not shown. This would explain how Jill knew so much about the zombies and the T-Virus. No mention is made of Chris Redfield or any of the other survivors. So the events took place, but the way they happened are drastically changed.
AThe blast from the nuclear detonation over Raccoon City catches the helicopter evacuating Alice, Jill, Angela, Carlos, and J.L., causing it to crash in the Arklay Mountains on the outskirts of the city. Two hours later, Alice is rescued and taken to an Umbrella research station in Detroit, Michigan. No other bodies are recovered in the wreckage. Terri's footage blaming Umbrella for creating the zombies and the T-virus is proclaimed a hoax, and Umbrella releases a coverup story blaming it all on the explosion of a nuclear power plant, noting that Jill Valentine and Carlos Olivera are wanted for questioning. Three weeks later, Alice awakens nude in a water tank. Dr Isaacs (Iain Glen) orders the water to be purged from the tank and Alice released. When they attempt to question her in order to find out what she remembers, Alice replies, 'My name is Alice, and I remember everything.' Clad only in a towel, Alice fights her way out of the hospital only to be confronted by dozens of armed guards. Suddenly, a car drives up and Carlos and Jill, disguised as Top Security Umbrella officers, collect Alice and drive away. Back inside the hospital, Dr Isaacs orders the guard at security gate to 'Let them go.' In the final scene, Isaacs says, 'Program Alice activated,' and a close-up of her eye shows a flashing Umbrella logo, while Alice sits silently, unresponsive to her friends' questions.
