- Omega Gamma
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It's not my job to disprove that your 'God' exists. It's your's to prove it does.
"Eímai ánthro̱pos. Eímai óla gia ména. Den ypárchoun Theoí ».
Omega Gamma
I'm Now just going right out there with wild speculation.
Provided Chief continues in the military (like he wouldn't), I think the UNSC will send him off to clean up the Covenant Storm with The SPARTAN IVs and the newly found survivors from Blue Team (surviving S3's get upgraded to S4's) and Red team (Alice, Douglas and Jerome from Spirit of Fire) while trying to pair him with a new AI. Initially they might try to pair him with a copy of Cortana but he absolutely refuse.
After a bit of time without AI assistance Chief realises he is slipping up without a AI and so agrees to do a trial with Cortana 2 but doesn't like how ghostly similar she is and requests a completely new AI (my hope is Roland).
The Cortana 2 Model may be created to try and emulate the memories and experience of the original Cortana 2 using recovered fragments but still subconsciously knows she is just a copy. This realization come to the surface and goes ape -blam!-/rampant due to a combination of this realization, the original Cortana 2's and Chief rejecting her, causing her to goes ape -blam!- crazy steal a ship (maybe the Infinity or even the whole UNSC fleet) and goes and finds then(somehow) hijacks an old Forerunner Fleet with maybe Prometheans.
She then goes to war with Earth.
Earth realises she's coming, prepares to try and defend itself but her forces are too great and won't relent to Chief accepts her as the real Cortana 2 and joins with her. Arbiter and his faction turn up at the request of Lord Hood but get their ass handed to them by Cortana 2 resulting in Arbiter's apparent death.
Chief to save Earth and it's Elite ally's, Chief goes to her agrees to Cortana 2's demands. Cortana ceases fire, uploads herself to Chief's armour/mind (causing chief to start going seven flavours of crazy in the process), initiates a random Slip Space jump to ensure the UNSC wont find them and end's up near the core of the galaxy where they find a Precursor relic.
Halo 6? Cortana 2 tries to treat it "Just like old times." He now has to fight Cortana 2 control over him/his suit. How that ends up, who knows?
[Edited on 12.03.2012 11:16 PM PST]