I recently noticed how much that game is like Neon Genesis Evangelion. They are fighting against near-divine beings in a distant apocalyptic future, with the Last Boss being more or less, God, and he's pissed (not to mention looks almost exactly like the Angel Ramiel, except yellow). And the pilots are young but still have the fate of the world in their hands, and go through quite a lot. Then the ending, it had similar bittersweet apocalypse with renewal, "Book of Relevations Armageddon" ending, in that at the end the said being succeeds and kills the last of humanity, but then after the dust settles, things are put in place for mankind and history to begin anew from the beginning, with a single man and single woman as their start.
Though I actually hated Evangelion, I did like Silvergun. At least Silvergun's version wasn't so horrifyingly bloody and had such disturbing monsters and nudity. Though I think the Silvergun Pilots had it worse than the NERV Pilots, for the NERV pilots still got to go to school and stuff between Angel Attacks, the Silvergun Pilots not so much because 99% of humanity was dead!
Though this isn't the first time I've seen a Ship Fighter game with a heavy and serious storyline, but it still makes this name notable.