These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Fridge Brilliance: It bothered this troper that Varvok and his Batarians were supervised by Zek and his pirate Kig-Yar gang instead of Sangheili overseers, who are typically the main commanders in the Covenant. Then I realised that this may be foreshadowing the Batarian's place within the Covenant caste system if they were to be annexed into the empire. They'd be above the Unggoy slaves, but below the Kig-Yar mercenaries. Note that in the lore these two species are the lowest ranked castes in the Covenant, which doesn't bode well for the future of the Covenant allied Batarians...
Nightmare Fuel: The normal creation of husks is disturbing enough, the Plague Spreader makes it even more so by making the conversion its main weapon via tentacle impalement, and it only takes seconds to become a husk.
When the Flood make their grand entrance, they do it with their usual Nightmare-tastic flair (the author outright says at the end of their introductory chapter that the Flood are why the fic is tagged with "Horror" as one of its genres). Particularly terrifying is Varvok & Zek's experience with them, including learning the hard way that the normal fiction rule regarding zombies doesn't apply to Combat Forms.
When the Flood attack the Plague Spreader, it tries to infect them, turning them into husks. It sort of works, but not really- they're not turned into husks, all it does is give the Flood armor making them harder to kill. Whoops.
Noodle Implement: In chapter 11, Zek's first mate Retz tells Varvok about a Kig-Yar erotic film that was horrid enough to make a San'Shyuum literally burn out their retinas after five seconds using a plasma pistol, getting it banned by the Covenant. The way he describes it draws some unsettling parallels to "Two Girls, One Cup."
The Woobie: Like most Unggoy, Kayap does not have it easy, and is pleasantly surprised by how well Liara treats him. Life still sucks for him as he's dragged into still more firefights and fails to convince his friends to defect to Liara's side, forcing him and his new allies to kill them.
It's almost amusing how he steadily gets angrier at how literally every other race in the Covenant seems to be getting upgrades that help them, while the best the Unggoy can get is lies, death, horrible medical experimentation, or some insane combination of the three.