Uprising is set 20 years before the first Contra, so it's set in 2316. Why he turns to the side using aliens for evil during Hard Corps is left unexplained. The same applies to Dr. Geo Mandrake, who's also in the game. Bahamut started the rebellion due to what was going on, and Geo Mandrake didn't know the extents of what his research was being used for until an outbreak started at the facility he was residing in.
I suppose they wanted to use the aliens to fight the government for some evil deed they were doing? Mind you, I've only played games in the main timeline up until Hard Corps, so I have no clue what goes on with Shattered Soldier or Neo Contra.