I disagree with Other M. While forbidden use of the power bomb is properly explained (it could kill potential survivors nearby) a plothole emerges for all of the other weapons when you die. Why would Samus take an order from someone who used to be her superior, when it will result in her death? She can't save anone when she's dead, and even worse, many of the monsters threaten the entire universe, not just the potential survivors on board. Holding back isn't really an option.

Even more jarring are the non-offensive suit capabilities like the varia and gravity suit, which couldn't harm anyone around her, but would save samus in extreme evironments (not to mention continually reduce all damage from enemies).

From memory, they also lose communication for a decent part of the game. Samus is a self-sufficient bounty hunter and should be making her own calls even more so in this situation. For all she knows, he's been killed (with a known assassin on the loose). Stop holding out for orders that may never come Samus.

It's simply illogical for Samus to put her life so on the line on the whim of an old superior. Sure, some restrictions made sense, but the majority just didn't.

....That still doesn't make any of those things we've mentioned plot holes, no matter how questionable or dumb they may be.  If someone does something that doesn't make sense to you, that doesn't make it a plot hole.

Scenario 1: We're on the 100th floor of a building. A bomb is about to explode on the second floor in 10 minutes, unless I can defuse it in person. Thankfully, there's a working elevator. I take the elevator down to the second floor, defuse the bomb with minutes to spare, we all go home happy, everything makes sense.

Conclusion: NO PLOTHOLE

Scenario 2: We're on the 100th floor of a building. A bomb is about to explode on the second floor in 10 minutes, unless I can defuse it in person. Thankfully, there's a working elevator. But for whatever inane reason, I'm holding an idiot ball. So instead of taking the elevator, I somehow run down 98 flights of stairs and defuse the bomb with seconds left, out of breath and sucking down wind like a vacuum. We all go home happy, but the viewer is still screaming at me and facepalming because I could have easily taken the quicker elevator like any sane person would. However, it's still possible in this scenario.

Conclusion: NO PLOTHOLE

Scenario 3: We're on the 100th floor of a building. A bomb is about to explode on the second floor in 10 minutes, unless I can defuse it in person. There are no working elevators. The doorway leading to the stairwell is locked. I spend the next 9:45 seconds trying to get down to the second floor, but it took me that much time to break open the stairwell door on Floor 100. We're doomed. The camera zooms in on the bomb's timer, showing tick down all the way to 4...3....2....1..... But wait, I defused it just in the nick of time, with a fraction of a second left. We all go home happy, the day is saved. But wait... How the hell did I get down 98 floors in 15 seconds!? That's impossible!

Conclusion: PLOTHOLE

Like I said, when you die, a plothole emerges.

One scene forces you to run through an extremely hot area, which is quickly killing you. You have a varia suit which will stop all heat damage, but choose not to use it and then die.

Also, the reason given for not using weapons is to not unintentionally harm potential survivors, how does Samus' non-offensive gear fit into this explanation?

And like I said, "It's only a plot hole if something that happened that logically should have grounded the events to a halt with no possible explanation as to why that event happened."

Dying is not a plot hole. Gameplay wise, you get a Game Over screen and you have to start from a save point. In the game's plot, Samus does not die.

You have an explanation as to why Samus didn't use the Varia suit: she was ordered not to use it. It doesn't matter how stupid the reason is. It doesn't matter how impractical it is to run through an area with extremely unsafe temperatures. As long as it is possible within the rules of that fictional world (not our world), it is not a plot hole.

I have an honest question: are you screwing with me, for the lulz? I'm not going to start throwing around the T-word, because you've been polite toward me. But I honestly cannot understand why you're arguing against the very definition of a concept. I understand you don't like the events of Other M, but you're arguing against fact. 2 + 2 = 4 is a fact and a law. 2 + 2 = 5? That would be a paradox. Your arguments for Other M is not 2 + 2 = 5.