The blue sun rose over the metallic surface of Cybertron its light shining off city's skyline. Many of the buildings were made of metals such as Titanium, Tridium or Trinium.

A comma in between "Cybertron" and "its" will slow the sentence down. You should give your audience time to let the sentence sink in.

The Cybertron War Academy was made of the standard Cybertronian alloys, what made the Academy stand out against the glistening city was the Dichroic glass. During the day it appeared red, and at night, it seemed to be blue – The change in colour had a somewhat sinister feel about it.

"Dichroic" doesn't need to be capitalized since it's a normal noun. In the second sentence, at "blue - The", "the" should be lowercase since it is not starting a sentence.

The Academy was bustling with Students, the word on the wind was war was about to break out and the Cybertronians were deciding their allegiances.

"Students" should be lowercase, it does not begin a sentence nor does it reference specific students by name.

Cybertronians were as much as one race, but also very much like different countries, with different traditions, methods, ways and each city-state had its own laws and methods of carrying out justice. A number of Conflicts had occurred between two nearby cities, one in which Megatron resided, and One in which Alpha Trion resided. It was argued that the laws for all of Cybertron should be streamlined. It was countered with the argument that the No Flying laws would impede the Seekers in their City of Vos, where flight was practised by almost every person living there.  The Decepticons, as they called themselves, were lead by Megatron. He spoke out against the Oppressive ways of the Autobots, how their ideals were suppressing the many freedoms his people enjoyed.

The first part of the first sentence is confusing, it sounds like you're trying to say Cybertronians are one race, but "as much as" doesn't make sense in the context of the rest of the sentence. This first sentence is also a run-on sentence, I would suggest a semicolon to break it up. How about "Cybertronians were one race, broken down into different countries with different traditions, methods, and ways; each city-state had its own laws for carrying out justice." I edited out the second use of the word "methods" and replaced it with "laws", which is almost synonymous with methods, but a stricter meaning. The semicolon also slows the sentence down.

Seekers flew in from Vos, and landed in a court-yard area. Many of the Seekers were showing their allegiance to the Decepticon Faction and were having the badge marked into their chromoderm. The tattoo was created by an electrical charge that changed the pigmentation cells within the Chromoderm. This was achieved by altering the signal the spark sent to the dermis layer. The effect was permanent until, for whatever reason, it was turned off again by a reversal of the procedure.

"court-yard" should be "courtyard" in the first sentence, it is a compound word. "Chromoderm" is also inconsistently capitalized; judging by how you used it it should be lowercase unless it starts a sentence or is someone's name, so I would suggest changing "Chromoderm" to "chromoderm" in the third sentence.

This is where I'll leave it for now, to give you a sense of my editing style. Let me know if you have any questions! I find it very engaging so far!