Yes, almost the entirety of the video is cutscene. At least they let you do something in the middle.
They don’t make it clear, but what you’re supposed to do with those supersoldiers is drive them off so you can get a clear shot at MB. (I looked this up after the third loss, because I was getting very frustrated.) You can’t beat them (they just heal when low on health) so it’s an infinite fight. It’s a good thing MB has so little health. I’m not sure it went to the cutscene on the first shot towards her, but it sure wasn’t many.
I don’t really have to explain what happened, because the game does a good job with it. A lot of it was also hinted along the way, so I wasn’t really surprised with anything except Anthony’s survival. I imagine that the reason we were so keen to take Madeline to HQ ourselves is that this general might’ve been in league with the Deleter; at least this way, we get to have records of what went down. I have no idea how Anthony managed to claw his way back up from the bottom of a lava pit, but I suppose with a freeze gun, he had a few options available. The plasma rifle was gone, but his goal was just to go places, and there weren’t a lot of doors on this ship that wouldn’t open until you killed everything.
Ultimately, it’s not a terrible game, in my opinion. It locks quite a lot behind story, which is more typical of Zelda than of Metroid, but it still has the pattern of exploring for upgrades. The story also wasn’t bad; it just doesn’t really match the sort of thing I expect from Metroid. The worst part, in my opinion, is that you can’t spam missiles. If you want to use missiles, you have to stand stock still, which is a great way to get hit—and you can barely heal at all in this game. The lock-on isn’t bad, but it takes effort to start, which is also a lot more than many other 3D games demand. The controls were the biggest detractor from the experience, in other words. At least it incentivizes using your beams?