Good thing first: I really liked this mission, although I’m not acquainted with the Transformers franchise. You are a good story-teller, but you need to pay more attention on reading what you wrote, or specifically ask for a beta reader who is good at the proof-reading part of beta reading (unfortunately, Skarmory isn’t, while I’m not good at the concrit and positive feed-back part of it). I’m sorry that I couldn’t respond to your beta request; I was in a hospital at the time, with my writing arm heavily bandaged.
Now the bad: If comments point out mistakes that escaped your beta reader(s), you are supposed to correct them (letting it stand as it is while we complain about bad SPaG in badfic would be hypocritical). Since you didn’t do this yet, and I don’t read the comments before I read the story, I was forced to take lots of notes that already had been taken, mostly by doctorlit. So here is what I got on first glance that has not already been reported to you:
The man got up and stretched a bit, scanning the room until his eyes fell upon a rather thick book next to the closed-door.
I don’t think that "closed door" needs a hyphen (what doctorlit calls a short dash), but apparently doctorlit doesn’t agree with me, or he missed this one.
Grant this boy, my son,/may be like me, first in glory among the Troj-.
This may be a minor issue, but if you want to be really good at SPaG, you should know that a mid-word-interruption is marked by an m-dash (like this: "—") rather than a hyphen. Unfortunately, you won’t find it on your keyboard, but you can find it in the GDoc menu (choose something like "insert" – "special character" – "punctuation" (left combobox) and "dashes" (right combobox); note that I don’t know the exact titles you will see because Google talks German to me).
It’s a short one but-wait do I smell spray paint?
Seeing a hyphen trying to separate words rather than connecting them is much more disconcerting than seeing a hyphen for a mid-word-interruption, so this should definitely be a dash. Doctorlit’s long dash would be the abovementioned m-dash again, but doctorlit is American. Since spellings like "colour" or "internalise" imply that you are writing British English, an interruption between words is actually different from an interruption mid-word and should use an n-dash – slightly shorter than the m-dash and surrounded by spaces – like I did here. (You can find the n-dash in the GDoc menu, too. Also, you may experiment with two consecutive hyphens to see whether and to which type of dash they may be transformed. Actually, my German installation of MS Word transforms a single hyphen to an n-dash when it is surrounded by spaces.)
doctorlit already noted the confusing paragraph structure that looks like Spensor finished is meant to be a dialogue tag attached to "How’s that concerning?". Since I guess that actually Phil speaks there, you may try something like:
While Spensor was speaking, Phil began gathering things for the mission. "How’s that concerning?" he asked.
Spensor finished, the readouts on his visor disappearing as he turned to his partner.
But then I’m not sure whether "Spensor finished" would need a callback to the action Spensor finished. Maybe you could just drop it and write something like The readouts on Spensor’s visor disappeared as he turned to his partner to lead into what Spensor said next.
Luckily we’re I’m going I don’t need feet!
You probably meant "where".
Why-oof!
This should be "Why – oof! " (British) or "Why—oof! " (American).
... he stammered as Phil handed him a bottle as he wrote down a charge for introducing ridiculous mythos.
We mock this kind of As Disease in badfic. It appears that Phil would need three arms to simultaneously hand a bottle to Spensor, hold a notebook, and type on the notebook’s keyboard or hold a pen to write into a notebook of the other kind. If Spensor is meant to be he-who-wrote-down-a-charge, we got a case of pronoun confusion, because "he" usually refers to the last male person mentioned; and I don’t believe that you meant this anyway. Replacing "as he" by "and then" would work much better here.
“Bleeprin kid. It ain’t my first rodeo.” Spensor gladly accepted Phil’s gift and began chugging. “Woah, save some for later.”
I’m confused about who is saying what here. Actually, I guess this should be three paragraphs, implying the shift of focus from Phil speaking to Spensor acting to Phil speaking again.
Phil paused and took a minute to internalise what she just witnessed, his suspicions confirmed.
Is Phil suddenly female? Also, Phil witnessing the events should have happened in past perfect, before he took a minute to internalize it. I’m not sure whether the correct word order would be "just had witnessed" or "had just witnessed".
He should have just come here himself and saved the bot some sanity…
This sounds to me as if Phil hadn’t come there at all and had just sent Spensor. "by himself" might work, but why not just write "alone"?
Unfortunately the were clipped by the POV change.
You probably meant "they".
Welp I’m at a loss. Maybe your fresh eyes-
Either "eyes—" (American) or "eyes –" (British; since it’s not mid-word, there’s a space and an n-dash, but not another space before the quotation mark).
Spensor thought for a bit, then gingerly took the the notebook from Phil and scrawled something down in it.
Repetition.
The the sue woke up.
Repetition again.
Spensor quickly transformed into the control panel form he scanned earlier ...
Should be "had scanned" (past perfect).
...or some kind nebulous generic area.
Missing word "of", but since this is in dialogue, it might pass as being Spensor’s fault intentionally written by you, if he hadn’t been talking quite accurate until now.
If all they plan on doing is going for a drive they’ll think nothing of a random dude dune buggying in the desert.
I think this should be "dune-buggying", but I’m not sure here. (For a moment, I wondered about a random dude-dune – as opposed to a gal-dune – buggying in the dessert, but that may really just be me.)
The sue’s replacement OCs all began talking about Lucifer their family’s relationship with him and the war in heaven.
You need a comma after "Lucifer".
“I don’t get it.” came his cybernetic friend.
If "came his cybernetic friend" is meant to be a dialogue tag, the period after "it" should be a comma. But it doesn’t actually work as a dialogue tag, and it can’t stand alone as a complete sentence, so I don’t have any idea what you are trying to do here.
With a reserved sigh he and his partner go to the next scene.
Should be "went" (past tense). The badfic’s present tense affecting the agents is not unheard of, but if this is what happens here and in other instances where your narration suddenly switches to present tense, it should be lampshaded in some way.
With renewed vigor they enter partway through the following chapter.
Should be "entered" (past tense).
Decepticons Starscream and Knockout introduce a human to their leader.
Should be "introduced" (past tense).
They read on as Jim informs Megatron about the current angel situation and mentions the names of Paige’s parents.
Should be "informed" (past tense) and "mentioned" (past tense).
I ever tell you about my friend Erector?
I think this should be "I ever told you" (past tense) or more grammatically correct “Did I ever tell you”, but then that may just be like Spensor talks?
They arrive at a generic beach. Oddly all of the Autobots are using holograms.
Should be "arrived" (past tense) and "were" (past tense).
Like one of those high end Japanese figu-hey wait!
Another instance where you need an m-dash for mid-word-interruption: "figu— hey wait!" (I’m not sure whether British English inserts a space after the m-dash, but it certainly looks better to me.)
Phil goes back to the Words.
Should be "went" (past tense).
The pair watch on as the Sue’s family reenacted a scene from Spongebob and Paige gets reunited with her girlfriend.
Should be "watched" (past tense) and "got reunited" or just "was reunited" (past tense).
They both wretch at the term...
Should be "wretched" (past tense).
By the power vested in the Protectors of the Plot Continuum, you, Pai-Spensor wait!
This is another instance where you need the m-dash for mid-word-interruption.
Hot plasma ripped through the Angel Sue as her lifeless, burned corpse floated to the ground, her non-canonical family disintegrating along with her as her influence slowly disappeared.
There may be other instances of As Disease I didn’t take note of, but here it sticks out to me. Since "as" implies simultaneousness, it appears as if the Sue was already dead when hot plasma ripped through her lifeless corpse, so what did actually kill her? Using "and" instead would work much better. The second "as" is okay, though.
HG