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.
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!