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Jill's arrival in Raccoon City is explained as her wanting to do some further investigations on Umbrella in Raccoon City.
It is revealed that the events of Resident Evil 2 were due to behind-the-scenes dealings between the US military and Dr. William Birkin, and Umbrella's refusal to allow that to happen. The US military is seen to have tried taking over Incineration Disposal Plant P-12A in their search for the G-Virus.
The doors in the RPD and the courtyard are blocked by some wooden barricades, this was never explained as to why they were barricaded or who removed them.
It is also revealed that the 5 other Tyrants were dropped off in the Incineration Disposal Plant in which they went in a fight with the US Military (with the first one being dropped in the Raccoon Police Station), this was the writer's decision to tie the story with the second game. According to an interview, Kawamura initially planned to tie it further by having crossovers and Jill infiltrating and investigating the underground labs but felt it would contradict the game's story too much and left it unchanged.
This game marked the first appearance of the Samurai Edge handgun, which would be deemed the S.T.A.R.S. standard sidearm later in the series.