Okay, normally I am loathe to do an '/thread' on threads, but right now I have three items that anyone can get, plus a web resource, that will definitively prove that regardless of fanboyism, the canon of Halo and the events surrounding Reach's fall are indeed not messed up, and do fit perfectly together. These are:
-The actual game, Halo: Reach.
- The book, The Fall Of Reach.
- The accompaniment to the game, Doctor Halsey's Journal (and yes, anyone can get that, it's been copied and put online by people and the details are widespread on the internet if you just Google it...).
Everything is explained within the canon, and the locations and knowledge of all important characters is reconciled by these three together. As for the timeline? I direct you to the web resource.
- A timeline of the Fall of Reach, backed up by Word of God (i.e. top Bungie and Microsoft executives and developers).
http://halo.wikia.com/wiki/Fall_of_Reach#Timeline
This explains everything, and shows exactly how it all fits together. I will answer here the three biggest questions that anyone usually has about the canonicity, to show how it makes sense.
1. Doctor Halsey had no idea that the Spartan-IIIs existed, yet she knew about NOBLE Team during the planet's fall.
Well, actually, she had already suspected the existence of a similar program to the ORION Project, but not the S-III project that Ackerson was doing. She never, EVER, mentions 'SPARTAN-III' during the game, and it's been classed as fact all along that she'd already had suspicions for a long time about a similar project, as stated with her finding the S-II and King Under The Mountain files in the book The Fall Of Reach, as well as the suspicions stated in her personal journal. She was still surprised, therefore, in Ghosts of Onyx, when she met Spartan-IIIs, because she didn't realise the full truth until then. It all fits with what we see in the game, and the established canon. No discrepancies whatsoever. Also, note that the armour of the Spartan-IIIs she later meets is very different to the NOBLE Team armour, which would also cause surprise later on...
2. The Pillar Of Autumn had already left Reach's system, heading to the first Halo, when the Covenant started to glass the planet, so how can it still be on Reach in dry dock during the game?
Again, another easy one. If you read the book The Fall Of Reach carefully, you'll realise that there is a decent amount of time where the actions of the Pillar Of Autumn during the space battle above Reach are not accounted for. This is just after John and Linda are sent to the Circumference, and the other Spartan-IIs are sent to the surface to defend the MAC Generators. During that time, when there are no Spartan-IIs on board, it can be inferred, and indeed was confirmed by Word of God, that the Pillar of Autumn received orders to return to dry dock on Reach to receive the partial Cortana copy, as stated in the game and Halsey's journal, something that was otherwise unknown to anyone but Halsey and (NOBLE Team) before then. It also explains why the Autumn left Reach without said copy, before getting it anyway when it returned to help in the space battle. After the events of the game, specifically the level 'The Package', the Autumn got the copy back and returned to the rendezvous point in orbit to await John and Linda's return from the Circumference.
Also, people claim that this isn't true because a Spartan-II is seen in cryo onboard the Autumn in that level of Halo: Reach, in an Easter Egg. Just for the record, EASTER EGGS ARE NOT CANON! That has been established ever since the Egg in the first game after the credits on Legendary, with Johnson and an Elite hugging, so this little tidbit can be disregarded. Again, the canon is intact and preserved, and the timeline is kept intact.
3. How are Covenant on Reach in July if the Autumn doesn't leave and the main attack doesn't begin until mid-late August?
Again, easy. It's explained in Halsey's Journal, and in the game, that the force on Reach near the start are in fact an advance force that made it to Reach by stealth. Indeed, that's the entire point of the first five missions of the game, fully half the Campaign, where you are trying to destroy the main methods of stealth infiltration on Reach and destroy the Covenant ships already present. The full invasion force doesn't arrive until straight afterwards, which is already August, as stated in the Journal, the game, and as was already established in the original book. The dates do match, check yourself if you don't believe me. At this point, the Pillar of Autumn gets the order to return to Reach orbit and help in the battle, thus setting the stage for the second half of the game and the end of the novel. As for the fact that such a stealth invasion is never mentioned in the original novel, it can be inferred that the attack was, until the invasion of New Alexandria (which happened only after the main attack and the Autumn's recall), kept hidden to avoid panic. The attack only occurred in certain areas, specifically near Visegrad (i.e. ONI's Sword Base) and the associated Forerunner installation, so was easily covered up until the decloaking of the Covenant stealth ship in orbit around Reach. This also explains why the Spartan-IIs weren't aware of the attack until later, and we also know that they already had another mission to follow which was important enough that it overrided the Winter Contingency, until the full recall after the full-scale invasion.
Again, canon intact, timeline intact. No discrepancies whatsoever.
By the way, if anyone wants to argue with me, then feel free to let me know your thoughts. I'll enjoy using established canon and logic to dismantle your theories piece by piece

. And with that I think I can safely say...
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