There's an alternate chapter that takes place in a modern day setting with the characters literally reimagined as part of a sentai team,
a whole alternate storyline where you play as Dorothy (who is surprisingly tough for a tiny, prancing girl), a stage where you can play as a group of regular enemies, and numerous alternate costumes of characters from other Konami games.
The first person shooter was originally supposed to follow a linear
storyline, then it was going to be an open world shooter, and now it's a reboot of the
whole series set in an
alternate timeline where the US's space program grows massively because JFK wasn't assassinated.