Here's my guess at the plot On earth the victory over the covenant has come at a huge price, so once humanity gets back on it's feet, people start to rebel. Like in the past, the UNSC turns to ONI for help and Colonel Ackerson (creator of the spartan IIIs) Creates spartan IVs. When earth starts to expand their reach once again, they find the planet Chief is on and find him fighting. Whom? monitors and, in the end, a precursor(Featured in the newest novel halo cryptum) . I think that since there is only 1 precursor, the trilogy will go much like the original Star Wars. First believing that humanity has won, then losing and learning more about the enemy, and finally, Defeating the enemy in the end. I have no reason for the reds and blues fighting, but this is a guess so take it as you will.
if you watched the legendary ending of Halo 3, Cortana says that she dropped a beacon, but it will be a while before anyone finds them. Halo 4 takes place 5 years later, so i dont think they will stumble upon MC and Cortana by accident. and like Radius55 said, Ackerson is dead.
If you read the book, you would know that the first active Spartan 4s were already deployed by 2553, which was they year the Human-Covenant War ended. Some of them were temporarily assigned to the UNSC Infinity before it was scheduled to launch. The Infinity was a starship technology demonstrator, likely using recovered technologies found during the war against the Covenant Empire and/or from Forerunner facilities and installations. The crew onboard of the infinity consisted of several SPARTAN-IV.Now also if you read the books, you would know that 343 Guilty Spark took over the UNSC Infinity so that he could find the Librarian.
My assumption is that the Librarian is hiding where MC and the UNSC Foward Unto Dawn land, 343 Guilty Spark will make his way their with the Spartan 4s onboard of the Infinity, and once the Infinity reaches the new planet, they will contact the UNSC and the ONI and thats when they will make there way to help out. That is also where MC is going to get the upgraded guns and his new armor. ***Speculation*****
Its an interesting concept. I've got to think that something will happen to save Cortana from going rampant; I know we played the majority of Halo 3 with no Cortana (sort of) but it would be odd to not have her be there in Halo 5 or 6.
In Halo 2's story mode, Cortana was tortured immensely by the Gravemind. and for those of us that actually watch RvB, the Alpha was also tortured immensely by Dr. Church, who is the director of the freelancer program. now after the Alpha was tortured by the Director, it fractured its self to protect its self, and split its self into different segments/AI which all inherited one trait each from the alpha. Do you think that, possibly, Cortana will do the same sometime in the trilogy? i too find it would be weird playing Halo with MC and without Cortana, so maybe when she goes completely rampant, she will fragment herself like the Alpha did? kind of like an Epsilon-Cortana kind of AI? Also, as a side note, Burnie (the creator of Red Vs Blue) confirmed that in the RvB Universe, Dr. Church worked with/under Dr. Halsey at some point, and for those of you that dont know, The Alpha was based off of Dr. Church and Cortana was based off of Dr. Halsey.
"Agent Washington has stated that Alpha is/was a "smart" AI, which would make it similar to Cortana. Now, however, it's current state is that of Church, in which many of the personality traits (including but not limited to rage, deception, logic, marksmanship, and creativity) have been separated into alternate AI's for field use. Personality traits of individual AIs may or may not have been copied from Alpha, as they could either be side-effects of being copied or of rampancy."
Now im not saying that the Stories will really meet eachother, im saying that the storys might have some type of relation. Alpha fragmented its personality traits into different A.I.s due to being tortured and possible rampancy. Cortana has been tortured, as i stated earlier, and is going rampant, so there is a possibility she might do the same.