We all know the answer to that one...

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.

Well,the Hyperion's New-U stations sometimes makes a comment in the lines of "Remember, this isn't canon.". Also it was explained repeatedly in many interviews that New-U Stations should be ignored by players as much as possible, since they're just a gameplay mechanic for respawning. IIRC no one ever talks about the stations in the game, just like if they didn't even exist at all.

Nuff said

lol as if there are video games, movies or books (ANY work of fiction) with no plotholes in them!

You just gave me an idea.

....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

But it is possible; What if it takes place in 3844 and you can teleport?

Glad to be of service, you heathen

Nope, takes place in 2031 when people are so ingrained into their cell phones that they are two stupid to figure out how to use a door without the help of an app.