There is a lot of tension in this story. I can tell someone got hurt bad, but I can't figure out who it is. There is urgency with the lack of good explanations.

But I'm afraid I still don't get it. Apparently we start with a nightmare about Ajax and Levy's last mission, and a hundred eyes standing refers to the Argus replacement, but I wouldn't even get this if I hadn't read Ajax's biography on the Wiki.

Ajax receives a message. Since he already joined Mathew, the message can't say that Levy woke up from her coma, and it can't be a message from Levy saying that she'll move to Floaters (or this interlude doesn't match the bio); I wonder what it actually says.

I guess that Ajax's memories while he goes to visit his friend in Medical appear incoherent to show a specific state of mind. So we get a continuation of the nightmare, where Levy escapes to medical, but then we get a flashback to events before the events of the nightmare?
An arrow grazed the girl’s cheek, followed by another feminine form flying over the Eyes. The boy then slammed into the Eyes, dropping a smartphone-like device in front of the girl.
Capitalizing the Eyes may work, because they are a stand-in for Argus, but why didn't you do this from the beginning? Just to confuse me?
Who is another feminine form? The Sue? Judging from the flashback below, wasn't the Sue chained to the bed when they charged her before the Argus replacement hurt Levy? So who shot the arrow? The Argus replacement?

The screamed occurred along side the sound of glass shattering. Wings appeared on the girl's back, and once blonde hair returned to blue. The eyes, not missing a beat, grabbed the wings.
Should be "scream", and we are back to non-capitalized eyes.

Then we are back from the flashback and in Medical, where Doctor Appleby may just have introduced himself and now shouts for a Defibrillator, and a draconian humanoid rushed through the still open portal into Medical? Or to the place in the badfic, where Ajax still is? I'm not quite sure about this.

And we're definitely back to the badfic, where Ajax has just killed the Argus replacement (while Levy escaped to Medical?) and now wants to kill the Sue, too. But his leg is hurt, and the Sue is advancing onto him (wait, wasn't she chained to the bed?), and there's the draconian humanoid again.
"Get to the portal," the spectacled Dragonborn said. "She’s okay, just get going."
I'm lost. Did the Dragonborn go from Medical to the badfic to tell Ajax that Levy is okay? Who is he? DIA – Special Response?

Ajax dispersed his scythe, and hightailed it back to the motel room they found the Sue in.
You may have meant to say "they had found" (past perfect) or I may be getting this totally wrong. Anyway, I'm lost. Are there two portals, one the Dragonborn just came through and another in the motel room (where the Sue should have been chained to the bed, or is this bed elsewhere?), and why must Ajax go to the motel? Can't he use the portal that's apparently right there?

In the final memory, Ajax arrives at Medical, and obviously Levy isn't okay, and apparently Ajax didn't kill the Sue, so his bio is a lie?

But I don't actually need to know what exactly happened on that mission to relate to the characters and feel their pain.

HG

*begins noticing tiny errors all of us managed to miss*