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The SII's mission was to go deep in to Covenant space and capture a prophet with the hopes of ending the war (Thought as we see later on, it wouldn't have helped). Cortana was loaded up with the UNSC's best infiltration programs, all their knowledge on the Covenant and their ships, as well as translation software.
She was also a "smart AI", capable of thinking and learning about a diverse number of topics, unlike "dumb" AI that were programed for only a few purposes, but still brilliant at what they were made for. Smart AI are also made from the neural pathways of a real human brain, which also destroys the brain in the process. What make Cortana even more special in that regard, is the fact that she was made out of a flash clone of Halsey's brain.
She was, at the time, one of the most important AI's ever made.
Halo: Reach introduced the concept that they didn't arrive at Halo by accident, but because Cortana found (or translated) the coordinates in the Forerunner ruin under the ONI base.
So that's why she seems so important now. In truth, it's just a plot device to connect to the first game.
concept was already in the books way before Reach the game was ever a thought
And happy holidays to you all!
Actually the only real retconning in Halo is centered around Halo: Reach and The Fall of Reach. No other books take place at the same time the games do, so there isn't much to retcon that way.
And even at that, IIRC the only real clashes in lore came from The Fall of Reach itself, largely being the discrepancies in the number of SII's available to be deployed on Reach. The SIII's presence is explained later as being a project that Halsey had no knowledge of until she met Noble team at Sword Base, but it is also heavily hinted in, I believe First Strike, that Halsey had begun looking in to them heavily after meeting them.
The events surrounding Reach make up a very large part of the lore.