- The BELIEVE Campaign was the result of an ONI campaign to hide the truth about the whole ordeal with the Master Chief and the rings. A romanticist version, much in the way some legends about historical people still remain. However, there is some truth: There WAS a battle at New Mombasa after the Forward Unto Dawn left, but it was a different Spartan, worn and depressed out of his mind with the loss of almost his whole family, using his squad leader's title for troop morale.

- Number of surviving and operative Spartans is classified to hell and back, and not even ONI knows how many are really in action. There were actually several off-shoot projects going on trying to copy or steal Halsey's success, with varying degrees of usefulness (HELLSPARTAN, HAYABUSA, FREELANCER, SPARTAN-III, etc). This explains the irregular numbers, and some programs not mentioned a lot in canon.

- Likewise, this would cause a small political incident called "Spartangate", in which all generations prior to the SPARTAN-IV are judged and analyzed because of their war crimes. (Stolen from something I found on Halofanon)

- Halsey isn't that stable as she seems, and neither are the SPARTAN-II trainees. To put examples: They picked up a kid that lived in the woods alone and had her mother and father die from the same disease, a girl that actually escaped training and saw her own clone, a bunch of troublesome little shits that even stole a pelican once, and even a Spartan that gets recurring dreams of Halsey, Cortana, and his mother turning into a blue lady.

- The Rookie faced the last Brute Chieftain on Halo: ODST completely on his own, mimicking how Edward Buck faced a Covenant Zealot by himself back at Harvest. While Edward Buck obviously received a lot more man-crushes after he triumphantly killed his foe, the Rookie kicked the Brute's ass, too.

-Likewise, the Brute Chieftain in question was a psychotic, unrepentant mass murdered that not even his pack liked. He had been following the Squad for a long time, and actually wanted to "play" with his prey. Before getting his ass kicked.

- The Rookie looks like Sean Maher out of armor, and Buck once called him "Jennifer Dylan" after he read his initials.

- SPARTAN-II fight like Monty Oum's characters... if he said the Freelancers were normal humans with powered armor, that would probably make the Master Chief Space Kratos. Hmm.

- The Master Chief found the terminals thanks to a geas by the Librarian.

- Noble Six wore a default black armor, but has used almost every piece of equipment known for Spartans to have back then. Even then, everything else about him was still classified to hell and back.

...

- Red vs. Blue is in some part canon. Project: FREELANCER exists along with many more programs trying to copy Halsey's own program, but it's a failed offshoot of the SPARTAN-II Project given everything that happened, especially with the whole "Meta" thing that was classified to hell and back.

- Likewise, Tucker is considered an honorary Sangheili, and even got his own battle poem describing the final battle against the Meta. Written by Lavernius Tucker himself.

- The Human-Covenant war was the result of a wish made by a Magical Girl wishing to a talking cat-like thing that humanity actually got to meet more alien species. Given how both universes run, this obviously backfired.