The remains of Raccoon city. Notice the three craters within a larger crater.
The Sterilization Operation was the final attempt of the US Government to "sterilize" Raccoon City. The President of the United States gave the military the order to fire lethal weaponry at the city in order to eliminate the dangerous mutagenic Tyrant virus. The mission was to fire a strategic missile into the heart of the city, destroying the city and the virus.
Portrayals
Original
In Resident Evil 3: Nemesis, it is shown as a single missile (armed with a top-secret new type of thermobaric warhead) impacted close to the Raccoon City Police Department, destroying the entire city and presumably much of the Arklay Forest.
Outbreak
In Resident Evil Outbreak and its expansion pack - Resident Evil Outbreak File 2 show their own iterations of the event.
In Resident Evil Outbreak, three missiles are seen striking the city, which causes an explosion shown as a mushroom cloud in the distance. In the game's epilogue, four missile craters can be seen: Three around the city and a large crater in the centre. This suggests that while the top-secret warhead portrayed in Resident Evil 3: Nemesis was used, another three missiles were fired, also.
In Resident Evil Outbreak - File #2, the ending is portrayed differently. People evacuating by helicopter in "Up and Away" will fly past a number of missiles strike the city. Coordination is shown to be from "Heaven's Gate", a military command centre in communication with a number of fighter aircraft which are firing their missiles at the city. Again, a mushroom cloud is seen in the distance.
Degeneration
In Resident Evil: Degeneration, one of the news reporters at the start of the film mentions that the red raging fire beyond the mountains behind her is "what's left of Raccoon City after the military fired a missile at it", while another reports says that "the missile was allegedly nuclear", again pointing toward the single missile, as opposed to the Outbreak depiction, and adding the fact that it was assumed by the public to be nuclear due to its true nature being top-secret.