This is story-related and unmissable, however, you are timed!
During the final mission, after destroying the carrier, you'll be flying a ridiculously powerful Manta, chasing Shin who is flying a Manta with a ridiculously strong shield.
You'll circle a volcanic mountain a few times, fly along a river a ways, do some more circles, go under the same bridge twice, then soon afterwards turn a corner heading toward the docks(you'll see partial arches about 200 feet high rising from both sides of the river but not meeting in the middle). If you have not shot Shin down by now and his Manta reaches the arches, you'll fail the mission, and if you don't reload your save soon enough, you'll have to watch the entire Campaign Fail cutscene.
It really isn't too hard to shoot Shin down, as your health regenerates and your gun refills automatically! One of the easiest boss battles I've ever seen. Just chase Shin and hold the trigger down.
Watch out for the plasma pulse bombs Shin drops and dodge those as they can do some damage, but otherwise I never was close to dying during this mission.