Good thing I get do-overs.
That fight was not first try, by the way. You might notice some anomalies with the timer in the top left: I cut out my first attempt at both fights. I lost to the AU while it was connected to the cable on my first go, but it didn’t make sense to keep the loss in for flow reasons, so I cut it out entirely. Losing to the AU sends you back to the Dark Samus fight (not the start of Phaaze, thankfully), so you’re not missing much. Just me struggling to understand how to fight the AU: I didn’t realize I could shoot the ports while they glowed yellow. It’s kind of a throwback to how I fared against Mogenar, what with my exposing weak points and then completely failing to actually shoot them. I didn’t struggle nearly as much with the Dark Samus fight the first round, but I did take longer than for the second, so you can see the increased Phazon meter when I’m scanning the AU, compared to afterwards.
With the AU downed, Dark Samus (bonded to it) and Phaaze itself (also bonded to it) implode, though thankfully Phaaze waits long enough for Samus to leave. As Phaaze is bound to all of the Phazon in the universe, that also makes all the Phazon inert, permanently ridding the universe of the threat it posed. Having never seen the ship in the last ending chasing Samus, I really did think that was the end for this series. It also wouldn’t have made much difference to me if I had seen it, since I’d never played Hunters or any 2D Metroid by the time I last played the Trilogy. I would have thought it was just some lore from a 2D game that I’d missed, just as I expected the line about Samus’s work just beginning was talking about other, non-Prime entries. I certainly was never expecting a Metroid Prime 4, and with the destruction of Phazon, I had no idea what open plot point they planned to use. I thought everything was wrapped up. I guess we’ll see what that ship is about in the next game!