Metroid Prime holds up unbelievably well under all this sequence breaking, and that's probably proof of the design quality. There is one situation, however, that can be triggered and prevent you from being able to complete your current game. It's explained here so that you know NOT to do this.
If you choose to pick up the thermal visor, make sure one of the two events below have happened already:
1) The hologram projector in Observatory has already been activated, and the ledges have moved out from the wall so that you can reach the top of the room.
2) The glass in Research Lab Aether has been shattered by a space pirate. This can occur from either side of the room; killing the metroid isn't necessary if you entered from the bottom door.
Getting the thermal visor before either of these happen causes the glitch. The enemies in most rooms change when you get it, and both Observatory and Research Lab Aether are among them. In the case of Research Lab Aether, the only enemies there from that point on will be shadow pirates.
Since a space pirate is triggered to break the glass and not a shadow pirate, the event is unable to happen. A similar thing happens in Observatory. The panel you scan to begin activating the hologram projector won't work anymore, so you'll be unable to reach the top of that room too.
None of this would matter if Control Tower wasn't in between these rooms, but it is, and the only way to get there is through one of them. The thermal glitch makes it so you can't reach Control Tower and get the artifact of elder.
If you happen to trigger this glitch, don't save the game afterwards.
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