I really hope someone upload video playtrought of later maps on Youtube.
Overall, Contra: Return is divided in several parts:
1. Galuga and Syberia assault. Bahamut is commander.
2. Second Alien Wars. Bahamut conflicts with Federation Goverment and hires Noimann. He is still protagonist.
3. Bahamut's rising. Sadly, I saw this part only in Chinese version. It seems, Bahamut with Noimann get info about Moirai Relic. Also Bahamut hires Deadeye Joe in this part.
Yes. Character stories, portrayals, roles, relationships, timelines, etc. differ greatly from the established lore. This will also allow/justify the inclusion of all the new characters. That's the reason why all the new "Return" pages were created.
Regarding to minor enemies and bosses, it is not necessary to create specific "Return" pages for them, just a subsection on their respective standard pages will be enough.