Einhander's Excuse Plot actually serves a purpose: to ensure your death. The Einhander missions are suicide missions with no chance of survival. You're supposed to be the same, except for the whole living through the experience part. The train mission was something Selene came up in a pitch to get you killed and collect data on you while they still can. The next two missions come naturally, since by surviving, you entered a base and have to fight your way out. By the time you escape the base, they've worked out a new plan which involves the ultimately inconsequential Climax Boss.
Doubly clever since Einhander pilots' non-survival is still useful, in the sense that they are used to build the ever-smarter AI algorithms for both the EOS fighters, as well as Hyperion. You simply happen to be the one-in-a-million survivor. Being The Empire, Selene does not exactly decide that you are no longer useless, but the opposite: you are so useful that you need to be killed to add your skills to the EOS' AI. After all, you just straight up and destroyed the majority of Gesetz' military force, imagine a thousand-odd force with your skills!
It's more of a meta-example, but the fact that the Earth forces all use German (not to mention having a vague Third Reich-ish angle) while Selene/the Moon uses English is in a sense reminiscent of World War II games, with Nazis as evil and the Allies as good guys. This also conveniently disguises the fact that Selene is The Empire and that you've been a pawn rather than a hero.
In the manual it is stated that you don't go alone to earth but with a squadron. When you die you aren't being revived/ being sent back to the time before you died, you are controlling one of the remaining ships in your squadron that has caught up to where you got killed. Essentially you only play the protagonist on the life where you finish the game!
Between the time that you destroy the Schwarzgeist, get turned into a moving target for the EOS, and initiated your one-plane Roaring Rampage of Revenge, one month has passed. Who supplied your food, ammo, and that new space-boosters?