Well, I thought I would have two new missions to read today, and it turned out to be one mission and the revelation that I am from the future. While I deal with that particular existential crisis, let me give you some concrit here.
The mission was very short. Not the story, though, the mission itself just took up a very small portion of the story. When I copy-pasted it into Word to get a better look, I found that out of the story's eleven pages the last time the Agents ended up actually going against badfic components was page six, and when you cut out the agents introducing themselves, it's really only three pages. That's an odd proportion, especially since the biggest canon breach was yet to come, which makes the whole After that, about all of it was "they talk to Makuta" or "they realize Makuta isn't affected by their neuralyzer"... and then they just leave him there.
The most powerful frequently Sue-targeted being in the continuum, and they leave him with full knowledge not necessarily of the PPC, but at least of Sues and the fact that inter-dimensional travelers enter Mangaia on a regular basis.
Take him to FicPsych and get that information out of him! The only reason that certain canons are allowed to know about the PPC is either a) they're omniscient so they'll find out anyway, i.e. Doc Scratch or Aslan b) they can recover from anything that affects them mentally so you might as well not even try, i.e. Jack Harkness and most drell (there was once a whole interlude dedicated to trying to remove knowledge of the PPC from Thane Krios, a canon character drell, because of how hard it is to affect their minds), and c) whatever is going on with Murdock and Gaspode, but I'm pretty sure that was made from one part their own mental instability and two parts Rule of Funny.
Frequently Sue-targeted individuals are not allowed to know about the PPC. The Sue controlling them can learn about the Agents through them, or if they are possessed or something, the wraith will know about it, which can potentially compromise people going on missions.
When Teridax is about to leave, he refers to them as "little humans". There are no humans in Bionicle, and nobody has ever appeared to Teridax out of their disguises. He might have been able to pluck the word from someone's surface thoughts, but he wouldn't know what it means.
Also, you never killed the Makuta replacement. The Rahkshi copies were killed by an angry Teridax, but the Makuta replacement was never dealt with, and given that he was connected enough to canon to quote Teridax's lines, he would have been able to retain enough Makuta cunning to shapeshift himself into something inconspicuous to hide. Maybe he did, maybe he didn't. It's a loose end, and when dealing with Makuta, there should be no loose ends, because a being with their level of raw power could grab it and pull until everything unravels.
With all that said, the dialogue was fun, especially Maggie's, and having the formation of the cavern separate the agents from their technology is a good idea that's simple enough in concept I'm surprised I've not seen it before now. Valon comes across very well as the over-excited newbie, and I can see a lot of potential for him, especially when compared to the absolute psychopath he was in his beta stages.