I feel that the story of Contra is actually fairly straight-forwards. The american version of the story is a bit more convoluted since they changed it from an already future-esque setting to a late 20th century one. Hardcore Uprising is an alternate universe prequel so it kinda stands on it's own. However I also feel that Contra 4 (awesome game to be sure) only adds to the confusion as it is a sequel to the american version of Operation C. In the Japanese version of Operation C there is no Black Viper. At least as far as Contra: Shattered Soldier's backstory history files is concerned. I am very curious as to what the Japanese version of Contra 4's story is since I can't seem to find it or any translations for it. Shiroi help! Please?
Contra 4's story is actually the same in Japanese, except that Mad Dog and Scorpion are not mentioned to be heroes of Operation C (implying the are new heroes to this game, since Mad Dog and Scorpion of Japanese Operation C ARE Bill and Lance).
What I mean by the lore being convoluted is that there are government conspiracies at work. There is a more complex reason for the alien invasion.
Emperor Gava/Red Falcon and all the aliens are just bio-weapons sent to Earth to recover the Relic of Moirai, stolen by the government (the Triumvirate) years prior to the first Contra. If I remember well they stole it from some ancient alien ruins on Jupiter, and triggered a defense mechanism that sent a bio-weapon to recover it. Said bio-weapon became known as Emperor Gava/Red Falcon. The Triumvirate know that, but they are not willing to have the aliens recover it. So they send Bill and Lance to deal with the EEEEEVIL aliens, both not knowing the aliens actually are not the villains.
It's a nice twist where the humans are the alien invaders stealing from other civilizations.
Oh that part. Some might see it that way and it's understandable. But it does set up nicely why the Moirai are dispatched to earth in the first place.
Emperor Gava/Red Falcon and all the aliens are just bio-weapons sent to Earth to recover the Relic of Moirai, stolen by the government (the Triumvirate) years prior to the first Contra. If I remember well they stole it from some ancient alien ruins on Jupiter, and triggered a defense mechanism that sent a bio-weapon to recover it. Said bio-weapon became known as Emperor Gava/Red Falcon. The Triumvirate know that, but they are not willing to have the aliens recover it. So they send Bill and Lance to deal with the EEEEEVIL aliens, both not knowing the aliens actually are not the villains.
It's a nice twist where the humans are the alien invaders stealing from other civilizations.
Yup! That's it in a nutshell ;)