It actually wouldn't make sense for Ella to fall to her knees if Nyx did it. You forgot that even the MC didn't fall to his knees when Nyx did it at Level 3. Level 5 Ella wouldn't fall because of that, even while weakened. That's why it's likely that Nyx's monsters that Ella had laying around stacked them on her. All of them being triggered as soon as Nyx comes within her proximity makes the most sense. Pair it with the letter and that she said she has a few monsters that made Nyx around, it becomes rather obvious.
Plus, once again, Nyx's power is green, not red. Ella is struck by Red Energy, not green during the scene that Nyx shows up at. We also know that spawns can have different colors from their monster parent's. Hence why I mentioned Nico and Hex having different colors or Ella and the 3rd or even Michael and 2nd. So it's more likely that the monster species that turned Nyx have Red Energy while Nyx, being a unique mutation, has green.
This would actually make more sense than Nyx doing it herself anyway. Malik and Nico would obviously notice Nyx using her mark on Ella, if it was her. That's on top of Deus and Zack noticing too with their powers. With her monster species doing it, it would make Nyx less suspicious, if they are working together because there's proof that she didn't mark Ella there.
This also doesn't contradict them working together and would actually cover Nyx, if they were. If they aren't working together, it still works. It works for both scenarios. I'm also still of the thought that she used that as a back up plan to Infiltrate HERO again and isn't actually working with Nyx at all but we'll have to see.
Hmm, I have some counterpoints.
1) Nyx mentioned that MC took it like a champ. It seems that his resistance to pain was unusual. Ella was also in the middle of doing something. Falling on her knees could easily be due to her losing concentration. There is actually nothing saying that Ella can't feel paralyzing pain. Level 1 MC's poison was enough to make her squirm during deadend3. Yes she was level 4 at the time, but still the power difference was huge.
2) I don't have any reason to believe that Ella is "struck" by something. That red miasma is her own expression of power. She starts summoning her power, threatens to kill them, but mid sentence she drops to her knees and loses her concentration. We've seen her do it numerous times, like when she evolves, when she transforms into that goat thing etc. There is no external agent causing that red miasma. It's all Ella.
3) MC wasn't struck by energy when he received the mark. Only the tattoo was green initially and there is no reason to assume it would glow through clothing. All Nyx has to do is raise her hand. Malik and Nico could completely miss it if she wanted to hide it but personally I doubt that she even tried to hide it. The only problem I find here is that Nyx wanted MC to strip so it may require a visual component, but it could also be for her own entertainment.
4) Nyx has claimed in the past that she likes to mark humans before killing them to gain more corruption. She is known to do this. Additionally Ella is a possible resource for HERO and even in the latest update Xanthe is still bitter for not getting info out of her. Ella and Nyx working together could still be true, but this explanation doesn't require it and perhaps Ella may even manage to convince Nyx to revive her.
5) Deus knows that Ella will survive anyway. He tells MC to not face her, keep his secrets close and don't tell her shit unless he is strong enough to impress, because her eyes see much but she doesn't have the correct understanding. MC is nowhere near strong enough to impress. This pretty much confirms that he believes Ella will come back and in full force. The only question is what Zack is going to do about it. He probably knows it too, and if Nyx killed her, it doesn't take a diviner to figure out who did it, especially if the body they have in captivity vanishes.