The second battle with Trask. In this battle, Ashley gains his Access power, and using Knightblazer, you utterly DEMOLISH it, despite it being a tough boss not an hour or so ago. What an AWESOME way to introduce the Second Hour Super Power!
The return of Brad. He starts by saving the entire party from being annihilated by Odessa's ultimate weapon. He accomplishes this by using a hand-held railgun, which is described as being normally vehicle-mounted(!), and crippling said super-weapon with only two shots. Then a flashback reveals he survived his earlier Heroic Sacrifice by taking down a perfect copy of himself and sacrificing it instead.
The FINAL Final Battle. You've just defeated the Embodiment of the Kuiper Belt, which was only possible via Irving's Heroic Sacrifice. The plot heavily implies that despite the good intentions and result, Irving's methods were wrong. You had no chance of subverting his machinations, however. Thus, as the party exits, they exchange words of melancholy. There is no sense of JUSTICE!. Then, BOOM, Ashley hovers into the air, heart exploding with power as Lord Blazer has FINALLY gained enough Negativity to break free. Ashley finds himself alone on what looks like a barren moon, with the Argetlahm embedded in rock a few feet away from him. Lord Blazer's voice booms from all around as he launches into a HUGE Hannibal Lecture, questioning and ridiculing everything the heroes have done so far. Ashley then gets up, goes over to the sword, and proceeds to proclaim that he fights "for a world that needs no heroes". Then pretty lights come out of his friends, converging on him. He prepares to draw the sword once more, and...cue the Boss Battle set to an EPIC! ORCHESTRAL! version of the game's theme song!