How to kill a plot? From what I think (key word is think. I may be wrong on this) it could be due to a number of reasons. Feel free to say I'm wrong and point out how cause it could be helpful for me when I (eventually) get to making my own comic.
Excuse me if none of these make much sense. I might end up rambling.
- Bad execution
This is probably the biggest one. No matter how good your idea or planning it out is, terrible execution can completely destroy all of that. Like it could start out well and then it becomes clear that the author is just making things up. Keep in mind, making things up probably isn't a bad way to go about writing your comic (and can even work wonders. I'm pretty sure One Piece, even though I liked its earlier parts, does this very often for example) but sometimes it can be done poorly. Two examples that come out of my head are Fullmetal Alchemist 2003 (specifically the last few episodes) and, from what I remember, Kingdom Hearts in general.
The obvious counter to this is to learn how story structure works and make sure the plot makes....sense I guess and has a sensible progression.
- Bad Improvising/Ideas coming out of nowhere
You also have to make the "ideas that come out of nowhere/improvisation" work to the plots favor. You also have to consider the medium the story is being told on.
Pulling ideas out of seemingly nowhere works for One Piece because they are in a setting where many fantastical things can happen. It works for the Mother video game series because the video game medium allows those optional elements to shine in their own way (if they are put to the side), the bizarre interpretation of the modern settings allow this to not be jarring, and because its Mother. And so on...
A bad example I can use is Homestuck (not that I think its terrible). The improvising elements, the characters doing random things (if that makes sense), slows the plot down to a snail's pace. Which leads to...
- Pacing
Spacing out the events in your story is important. I'm not really sure how to explain this one, someone else is probably better qualified. But I do know that its important to manipulate how you use your pacing.
A slow pace, is probably best used early on but making it slow later on can work (though I think its difficult.) and making the entire plot slow can work as well. Its mainly used to explore the characters, their motivations, backstories, personalities, likes, viewpoints, etc. Anyway, I think this could be best used to explore the characters in the story.
Best (positive) examples: Hunter x Hunter (Chimera Ant arc), Persona 5, Kubera (from what I've read)
However, a slow pace can leave a story feeling...aimless I suppose. And taking a bit too long to get to the next plot point with no purpose (keep in mind that the positive use of it can have people saying this as well. It doesn't mean its bad). In other words, the plot can become a slog to get through and (as you put it) stagnates.
Best (negative) examples: Homestuck's approach to pacing (though sometimes it can work)
Exceptions to the rule: Mother 3. Depending on if you explore or not.
A fast pace can lead to a fast moving and energetic plot. Best used if you want to put more focus on the plot. Bad fast paces lead to some plots becoming, as you put it, "complete nonsense". I don't have much more to say than that I suppose. And i don't have many examples. Someone else should probably cover pacing...
That's all I can think of for stuff that can kill a plot.