Chapter 1 edits, part 4

Much had changed for Starscream when he arrived back on Cybertron. There had been significant political upheaval. Gladiator gone Politician, Megatron was bringing people together to fight back against their neighbours who wished to impose their wills and ways upon the provinces near them.  Starscream, as soon as he returned to his home world after a decade of mentally scaring “solitary confinement” in space, compiled his report to submit to the University at Crystal City. What happened at the University devastated him as much as losing Skyfire... Perhaps it was the rumour of war brewing, Or perhaps it was that Starscream was a Seeker, a race of Cybertronian who were flocking to Megatron's banner or perhaps it was that Starscream survived where the brilliant  Skyfire had not. But the University revoked Starscream's degree, 'tore up' the report and promptly kicked him out.

The first two sentences can be merged; replace the period after "Cybertron" with a colon to link the two. I suggest a colon because using it leads the reader into the reason why much had changed. A semicolon would have slowed the sentence down, but that's not necessary for what you're trying to say. "Gladiator gone Politician" needs to be hyphenated to show the progression, like this: "Gladiator-gone-Politician"; you can also remove the comma after "Politician" to show that Megatron is being immediately referred to. The comma slows the sentence down and is unnecessary. Change "mentally scaring" to "mentally-scarring"; they hyphen is used for the same reason I mentioned earlier, plus you misspelled "scarring". "Or perhaps" should be changed to "or perhaps" since the word "or" continues a sentence. Change "banner or" to "banner, or" to slow this sentence down, it's really long, but the comma will keep it from being a run-on sentence. You also have an extra space in between "brilliant" and "Skyfire". Why is 'tore up' in single quotes? Is it to symbolically show what the University did?

Suddenly without a certified profession and now homeless, as his residence had been taken by the city and sold while he was “lost in space” and without any friends or allies, Starscream felt like his world had been spinning out of control. He contemplated his options remove his T-cog and plummet to his death by leaping off a chasm ledge, or join the war effort. Being that the Autobots had elected to remove his status Starscream decided between ending it all or joining the Decepticons. He was now without doubt a pauper once more. Ending it all did not appeal to the Seeker. He had strong survival instincts. His ability to adapt to meet the needs of an ever changing situation, gave him the ability to  look past the desperate moment and see that there could be a future ahead of him in an upcoming war. If anything, there would be more dignity and honour to die in battle rather than die by a cowardly and pointless act.

Add a colon after the word "options" to show that it leads into what you describe following it. Change "ever changing" to "ever-changing" to link the show the progressive state of the adjective. You can also remove the comma after the word "situation".

The bronzed gate of the War Academy beaconed him in, he grabbed the few scientific tools he had, the single journal he had been recording the details of his existence and quietly walked into the Academy. There were so many people around and Starscream felt a bit ill at ease. He had been on his own for a decade in space, having other beings around him felt strange -  being on solid ground still felt strange. He walked up to the clerk who was registering applicants.

By "beaconed" I assume you meant "beckoned"? You can also end the sentence after "beckoned him in", otherwise you have a run-on sentence (sometimes it's better to slow a sentence down with a period, comma, colon, or semicolon, it just depends on the situation. That's why I suggest many different methods). The last part of the sentence about the journal seems like it's missing something, it would sound better either as "the single journal he had been using to record the details of his existence" or "the single journal he had been recording the details of his existence in", your choice. You can increase the impact of the strangeness Starscream is feeling being around others on solid ground by changing "having other beings around him felt strange - being on solid ground still felt strange" to "having other beings around him felt strange - being on solid ground felt stranger still". By changing the end I emphasized the strangeness he felt being on the ground was harder than being around other beings by using the stronger adjective "stranger" over "strange".

“Scientist is enough,” the clerk said holding up his hand to stop the Seeker from continuing. It might have been just as well. Starscream was about to launch into how he was just recently stripped of his degree by no fault of his own. “Any other Skills or abilities?”

I'm pretty sure "Skills" shouldn't be capitalized, I can't think of an instance in the G1 canon where it was ever capitalized.

“Err...flight would be obvious -  I can emit a low level Electro-Magnetic Pulse -  its not very focused, so I can generally neutralise anything that that is directly touching me... – That's it I fear. I am also a meticulous record keeper.”

You should always have a space in between the end of an ellipsis and the next word, so "Err...flight" should be "Err... flight". You forgot the apostrophe in the word "its" so it should be "it's not very focused". You use "its" to describe the possession of something, while the apostrophe shows the combination of "it is". Change "anything that that is" to "anything that is" to remove the duplicated word. Lastly, the hyphen isn't necessary after the ellipsis for "me... - That's it I fear." The ellipsis shows his thought process has trailed, but the hyphen (which in this case shows he's interrupting his thoughts) isn't needed because the ellipsis implies he's naturally let his thoughts lead him to the conclusion that he listed all his abilities. An example of what I mean is if Starscream had said this: "I can generally neautralize anything that - that's it I fear!" Can you tell he's interrupting himself, keeping himself from revealing the extent of his abilities for whatever reason? The hyphen is a classic interruption and linking grammatical tool.

“Your age -  approximately”
Starscream tilted his head smiling in a youthful manner. “Nine-hundred and fifty-three thousand years. Give or take a few hundred.”

"Your age - approximately" should have either a period or question mark to show the end of the sentence. I'll leave that up to you.

The clerk wrote the age down, rounding it up to the nearest million, filled out the rest of the form.

Since the last part of the sentence describes the ending action, you should add the word "and", changing it to "million, and filled". The lack of "and" implies the sentence continues, but it doesn't.

I've got to take a break, sorry this is taking so long!