- Hoggs Bison
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If I had complete creative license-- including throwing away canon completely...
Exposition:
Master Chief and Cortana continue to drift towards the mysterious planet. Back on Earth, ONI and Halsey are busy analyzing info from the Halo rings, Ark, UNSC helmet footage, and other sources. Through analysis of the radiation on the FUD, they realize the slipspace portal was rerouted... and Cortana is the only one who would have been able to do it.
The UNSC Infinity has been in development for years; its purpose is to serve as a mini-Earth, complete with cultural, historical, and scientific data. Its mission is to explore space, to understand the universe around us and engage in diplomacy with any aliens we might encounter; essentially, its mission is to avoid the catastrophic damage that has been inflicted on the human race for so many years.
But there's something it needs to find first. Cortana is Earth's single greatest source of knowledge on the Covenant and, more importantly, the super-advanced Forerunners. Realizing Cortana is entering Rampancy, Halsey builds a new AI to assimilate Cortana's data... and then destroy her. The Spartan IV's, armed with Earth's most advanced arsenal, are tasked with delivering and retrieving the AI.
The UNSC Infinity and its crew catch up to the FUD as it nears the mysterious planet. Chief is awakened and taken on board, but Cortana is nowhere to be found. The New AI takes her place for the time being, and Chief receives his new armor. Requiem's gravity well opens and draws the ship in.
Rising Action:
On Requiem, the UNSC are pleased to find that the Infinity has incurred no significant damage. The Chief and UNSC hatch a plan to find Cortana - for their own reasons, though Chief doesn't know theirs - and they follow a distress beacon coming from the center of Requiem that the New AI detects. They fight Prometheans along the way.
The Chief is the first to get to a central structure, and he's immediately separated from the rest of the UNSC. The New AI is inserted into a nearby data port. As she begins searching for Cortana, she shows up in a port at what appears to be the center of the room. She's in bad shape, and begs Chief to rescue her by activating a release module. Before he can do so, the New AI begins fulfilling her mission: assimilation of Cortana's data... and obliteration of the empty shell. Chief attempts to stop her, but a Promethean contingent is summoned to get in the way. He breaks through and activates the module, sending tremors through the room and revealing it to be a massive sphere.
Cortana is suddenly revitalized, but her voice seems different, if familiar. Chief recognizes it as Guilty Spark; the monitor explains how he was able to preserve his data core and take over Cortana, rerouting their destination and sending them to wake his masters. The room is a huge cryo chamber, housing hundreds of Forerunners.
Climax:
Spark/Cortana easily destroys the New AI, and spark ejects Cortana, leaving her to waste away as Spark absorbs her architecture to rebuild his. Chief escapes and meets up with the UNSC: they hatch a desperate plan to stop the awakening by interrupting the procedure right as the life support is shut off, thus killing the Forerunners. Though they sustain heavy losses, they are successful... or so they think.
One Forerunner, their leader, has survived; he summons Spark to his suit, which seems impervious to damage. The Didact then heads to a control room, planning to recalibrate the Halo rings to destroy humanity once and for all. He leaves the Prometheans to finish off the ragged group on Requiem, which, as a shield world, is protected from the blast.
Falling Action:
Cortana reappears, having used bits of New AI's architecture and whatever else in Requiem to piece herself back together. It's decided that Chief+Cortana will go after Didact+Spark while the UNSC hold off Prometheans. Lots of Spartan IV's are killed as Chief frantically makes way to Didact's Control Room. Spark attempts to block Chief by destroying the path; Chief grabs a Warthog and plays through Halo 4's iconic Warthog Run. They reach Didact, and an epic battle between two seasoned warriors and two seasoned AI's ensues. Chief seemingly emerges as the victor and inserts Cortana to stop the countdown, thus saving humanity in the nick of time, just as they always do...
...But not this time. They watch the monitors in horror as the Halo rings detonate and the human race is reduced to the few hundred on Requiem. Didact reawakens, having occupied the Chief long enough to let the rings fire. Now exercising his full strength as a Forerunner, he crushes Chief's armor with his bare hands and gashes his body. He attaches Cortana to Chief and throws the mangled body to the eager Prometheans below. He and Spark leave on his personal warship to awaken Forerunners on other worlds.
Resolution:
Chief and Cortana are rescued by the UNSC, who are now aboard the Infinity; Cortana, in better shape, is informed by the ships medics that even if the Chief can be saved, he will never quite be the same. The small group, now part of a truly endangered species, leave Requiem as they are pursued by Prometheans. They realize that the galaxy is no longer safe for them: there are no more safe places to hide and, just as the human population has been so quickly erased, the Forerunner population will soon quickly jump.
Cortana proposes an unlikely safe house: while in Requiem's system, she picked up a Reclaimer symbol attached to a pair of coordinates she had no knowledge of. The UNSC make use of Requiem's massive energy stores to create a slipspace portal that will lead them out of the galaxy itself...
[Edited on 12.31.2012 11:57 AM PST]