You have the plans for Halo 5 right in front of you. You can alter it, keep it, or completely scrap it. You can also do anything to the people that work at 343i.
What do you do?
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First off, make it so that I'm in charge for life or until I choose to step down and that I can never be fired or otherwise removed from the position of overlordship with Halo. Then, promptly fire Brian Reed....preferably out of Bungie's giant slingshot aimed at the sun, ban Karen Traviss from ever touching Halo or getting involved in the creative process for it ever again. And then, declare pretty much every single thing 343i has done since Glasslands came out to be non-canon and throw it out completely, maybe have a mandatory celebration where a copy of each of the offending works will be burned on a massive bonfire where we'll also be burning Frankie in effigy after demoting him to janitor/errand boy. And then, we proceed to start over again from the end of Halo 3 and where it left off, keeping everything true to canon. I'd talk to Greg Bear and ask him what he had had planned for Silentium before 343i came along and made him change a bunch of stuff (as I'm sure they did since many of Bear's plot-threads were seemingly abandoned or outright contradicted in Silentium, there is no other reason for delaying the publishing and bumping back the novel for so long just to change the cover and for minor editing) and just the rest of the Forerunner Saga in general, and if it's good and fits let him write what he would have written before. Everything would be made sure that it fit within established canon from Bungie's run on the series. No "all Elites hate humans and always have, and they're now just looking for any excuse to go to war with them again, the only reason that any of them want peace at all is just so they can rebuild their own technology and society before trying to exterminate the human race again", or "every Covenant species is so idiotic, incompetent, and idiotic when it comes to technology that they couldn't even tie their own shoe without the Prophets' help". Elites will still be a major power spanning the majority of the Orion Arm within the galaxy, though it's only natural that they'd have some difficulties in handling technology on their own their economy or military prowess would not be completely crippled with billions roaming around all of the colonies within Covenant space aimlessly wandering around or sitting lazy in their keeps and wondering what the -blam!- they're supposed to be doing now. The majority of Elites will have a great deal of respect for humanity and either like them/be human sympathizers, or at worst just not want to fight with them anymore. The extreme minority are those like Jul who actively want to continue fighting and slaughtering humans down to the last child. There won't be any "ONI knows absolutely everything and can do whatever the hell they want to whenever they want to whoever or whatever they want and no one will ever know or ever be able to stop or touch them" so changing/removing that one little detail means no Halsey bashing whatsoever, Halsey remains free (because arresting or imprisoning her leads to too many questions and possible security breaches involving the Spartan II Program) along with everyone else rescued from Onyx (this would most likely be it's own book, there'd be too much else going on leading up to Halo 4 that'd need to be worked on for it to be incorporated into another story), officially ONI and everyone working for them will be working to destabilize or destroy factions like the Servants of Abiding Truth or all of these other sects of radicals that are left over from the collapse of the Covenant and weakening/completely destroying their power base. If the story arc revolving around Kilo-5 and their efforts to destabilize all former Covenant species whether they're allies or enemies of humanity is even included, it will eventually be discovered and all of those involved/responsible will receive the proper consequences for their treason. And then, absolutely most important of all, everyone who is a returning character and previously existed within Bungie's games and books will be in character and behaving exactly as they should. People like Lord Hood who were Halsey's friends and allies will not suddenly no longer give a shit about her and just let twisted devils like Parangosky do whatever the hell they want and break whatever laws they want in order to get back at Halsey. The Arbiter won't be a complete wimp who just hides in his keep at the first word of an angry and disorganized mob. Halsey won't be some twisted, heartless ice-queen who only ever cares about science or what she can learn. Mendez won't suddenly and inexplicably hate Halseys guts and act like a completely hypocrite. The Didact won't be some evil, mustache-twirling villain that hates all humans for absolutely no reason whatsoever and cackles maniacally at the thought of kicking puppies. And so on, and so on, etc. etc. ......I'm sure you all get the idea. Everything will be kept as closely to canon as is humanly possible. I'd regularly ask the opinions of guys still in Bungie (like Jason Jones and Marty O'Donnel) or formerly Bungie employees (like Joseph Staten) their opinions on the way things were being done or how they fit in with canon and the rest of the series. I'd probably hire the guy who did the music in Halo Wars to do the music and be lead composer for the games or the guy who did Spartans Ops. Maybe send whoever I hired off to learn from Marty and ask if he'd be willing to take them under his wing for a while in order to make sure that the music stayed true to the series and fit in with the rest of the games. Find out from Eric Nylund how he would have concluded the story threads leftover from Ghosts of Onyx and maybe try to coax him back to write that story himself [i]or[/i] try to get him at least involved with the whole series in some kind of advisory capacity. So yeah, that's what I'd do.