Chapter 3 edits, part 1

“that means no fuel for days....going hungry, I hate going hungry.”

That's an improper ellipsis, it should only be three dots.

“Yeah, I can, its how I can travel through space-but I can't tell you how.

Change "its" to "it's".

“I suppose we ought to report to the Sergeant; before he hunts us down.”

The semicolon is an unnatural break. An ellipsis would be good there instead! You could also add emphasis to the word "before" for extra flavor. Italics is a good option for that, or bolded text.

“I got a feeling he's gonna be on our case from here on in,”

That should be a period at the end of that sentence instead of a comma.

“Yeah no thanks to you and those up-side-down insignias

"up-side-down" should just be "upside-down".

That it was merely a method of seeing how badly you wanted to stick around with me,”

"stick around with me" sounds awkward. Can you send some suggestions my way for what you'd like to say? I want to try that rather than suggest my own word choice. ;)

You choose to follow my lead and now are marked as a group,”

"choose" should be "chose" since they made this decision in the past. Instead of "now are marked as a group," how about "now we're marked as a group,"?

his voice was low barely audible to Thundercracker who stood nearby.

This sentence needs a comma! "his voice was low, barely audible"

“It may be prudent that we maintain this new alliance to get the three of us through this academy alive.” he said raising his voice loud enough for Thundercracker to hear clearly,

Your comma and period should be reversed here: “It may be prudent that we maintain this new alliance to get the three of us through this academy alive,” he said raising his voice loud enough for Thundercracker to hear clearly.

“Again this choice is yours to make – we don't have to ever become enemies.”

Is that foreshadowing in the latter part of that sentence? Seems like an odd thing to say out of the blue. Even with the context of the next sentence it sounds odd.

“If we can form some sort of 'trust' between us, make a pact now, agree to back each other up, thick and thin we can get through this alive and perhaps come out on top.

Change "up, thick and thin" to "up, through thick and thin". The expression is "through thick and thin", hence the correction.

First part done!