Here's how I see it going down. Scar-face gets in his TSF. Starts off strong. If he turns out to be the Japanese instructor from the first two episodes, there'll be a moment where this is revealed to Yuki, which causes her to lock up, because we all know she locks up when the shit hits the fan.
If he's really the end boss, Yuya ends up finding some inner reserve and becoming one with is machine at the sight of Yuki's imminent death at the hands of Scar-Face, and comes from behind to destroy him and cement Yuki as a permanent member of his future harem. Not that it was ever in doubt, of course.
If, however, it's really the BETA who end up being the end boss, I can see Argos Flight taking Scar-face down collectively as a team, with a few witty platitudes of how they're all there for Yuya, after Yuya first attempts to be the lone hero, then when the BETA show up as the real end boss, in numbers far larger than they ever could imagine and all hope seems lost, Yuya has his moment where he becomes one with his machine and convinces Leon to abandon his American mission to set off those bombs, and the two shout heroically like men as they show of their mad skillz to turn back the BETA threat and lead their respective flights to glory (while sticking it to those power-hungry Americans).
On a side note: no microwave gun?
End scene being some cryptic statement from pretty-boy behind the scenes as a hook for anime viewers to get into the Muv-Luv franchise.