inb4 TLDR
Dream Plot: (which is sure to eventually devolve into derivative garbage by the end of this post)
Prologue:
Following the events of Halo 3 the Humans and Covenant create joint task force/coalition assigned with tracking down and annihilating all traces of the flood throughout the galaxy. The massive war fleet, whose ships are the product of human, covenant, and forerunner engineering set out to destroy all shield worlds and Halos completely - not risking going to ground and setting the flood loose.
The fleet most notably contains Buck's ODST squad, Admiral Hood, CPO Mendez, veteran Spartan 1's, surviving Spartan II's and III's, the Arbiter, Half-Jaw, and other elite and senior personnel. The fleet's first task is to investigate the cause of a massive supernova in deep space that they believe was a destroyed Shield World.
While heading to the destroyed Shield world, they pick up a distress signal from the UNSC Spirit of Fire - which, after the events of Halo Wars was drifting in space without a slipspace drive (and until this point thought destroyed and all hands lost to the UNSC).
Captain Cutter, Professor Anders, and remaining Spartans are still alive on board - they strip the ship of its leftover supplies and armaments and join the fleet. While they were drifting in space they managed to detect a faint and fragmented transmission - most of the message was too garbled to be reconstructed, barely managing to obtain partial coordinates for what they believe to be a Shield World bigger than the one they destroyed during the events of Halo Wars. They hand the data over to the fleet to be analyzed by the dozens of AI present on the fleet. They manage to reconstruct most of the message and find the coordinates to the massive Shield World/Forerunner colony world as well as a distress call sent by Cortana saying that the Chief is alive and they need rescue. The fleet then head off to find Cortana and the Chief.
The following could span the whole trilogy, probably into the next console generation:
Act 1:
MC and Cortana enter the shield world and crash land. They exit the wreckage and find themselves in the dyson sphere, a vast world built by the forerunners as their escape from the flood. They explore and investigate the planet, slowly learning that this installation is the dyson hub that connects all Shield Worlds to each other - all while fighting ancient-proto sentinels charged with protecting the central mainframe that runs the entire network of shield worlds.
All along the way Cortana deteriorates further and further, refusing to be transferred to the Forerunner network fearing that she will go completely rampant and lose her sanity. As they uncover more and more of the secrets of the Forerunner, they eventually reach the central hub for the Shield World. T he Chief, with direction from Cortana, gains access to the mainframe with his ancestral DNA and finds out that Dr. Halsey and the remaining survivors from the battle of Onyx made it into their dyson sphere and have sent a distress signal. Chief makes contact with the Onyx survivors and open a gateway, allowing them to enter the mainframe of the hub. Once they get there, something goes horribly wrong and all of the gateways to the other shield worlds open up. The network detects that the flood was released, a Shield World and a Halo destroyed, the Ark activated, and Earth contaminated with the flood. The AI running the hub believes the network to be in peril and activates radical extermination protocols and sets the entire network of Shield Worlds for destruction and remaining Halos activated.
Dr. Halsey believes that the only way to stop this from happening is to insert Cortana in the mainframe, as she possesses the most knowledge of forerunner systems and despite her deteriorating condition - is the only shot they have to destroy the forerunner AI and stop the annihilation of the known universe. After Cortana enters the system she reconstructs and repairs herself by tapping into a small portion of the infinite computing power on the forerunner network. She disarms the forerunner AI and absorbs it - thereby stopping the countdown and gaining control of the network. The celebration is short lived when Cortana suddenly snaps, the near infinite knowledge and processing power she has gained throws her into fullblown rampancy. Largely incoherent and muttering about things that the humans cannot comprehend, she slowly regains normal speech. In a cold voice she proclaims that she is God and knows the secret to immortality. She then states that the humans cannot inherit their legacy from the Forerunner because she has claimed it for herself and that she will not let them interfere with her plans. And with that she teleports the Onyx survivors and the Chief to opposite ends of the dyson hub - but takes Dr. Halsey prisoner, as she is integral to Cortana's plan for immortality. After the credits the rescue fleet arrives in orbit to find the world hostile.
Act 2:
Cortana reveals to the player that the first sentient race of beings in the universe created a race of machines in their image. This race of machines destroyed their masters and after millennia were left derelict. After the forerunners evolved they discovered these machines and created their own highly advanced technology, yet knowing through records the fate of their ancestors - they sought to place strict controls on AI and machinery - and refused to fuse man and machine together for fear of what they might become. Instead they use this technology to further enhance their own physiology to reach the peak of biological evolution. In this quest to reach godhood, one group who views that biology is the superior create the flood while another seek to augment themselves heavily with machine technology from the ancient machine race - who they viewed as the most dominant lifeforms in the universe. However before the latter group could achieve their goal, the flood were set loose by a rampant AI and ...the rest is history.
Cortana discovers the project files from the failed proto-machine/forerunner project and in the heart of the dyson hub finds preserved samples of the proto-machine race, flood, and intact cryo'd forerunner specimens. She retrieves them all and begins to create her own twisted army of machine/flood/forerunner beings as prototypes for the indestructible and immortal form she will inhabit. The player progresses through the game as Chief (lone rambo-style FPS gameplay), a TBD Spartan II and/or III from Onyx (3rd person tactical squad-based combat), and the fleet (space dogfighting and RTS battles) fight Cortana on 3 fronts and seek to rescue Dr. Halsey and prevent the destruction of all life in the universe. [though knowing Microsoft they may try and split this into 3 games released in somewhat parallel in the 360's lifetime that together make Halo 5...or something]
Aaaaand I'm too tired to think about what happens beyond that @_@lk asjghflkjagfkjlsagflkhjsagflkjhsagfljhsagfljkhsagflkhsagflkhjsagfjkhasgfjhasgfljhasgfljkhsgaf too much bulls***