Well, Jun is confirmed to be the new recruiter for Spartan-IVs, so... :P
There's a topic over on the Halo 5 subforum about someone wanting Halo 5 to have RPG elements. I generally think it would be a bad idea for a conventional Halo game to have RPG elements, but if 343i were to make a sequel to Reach (so long as they went back to the gritty and 'realistic art design)...
Well, I could certainly see you playing as a Spartan (II or III) or a marine/trooper/ODST trapped on the planet AFTER the Covenant victory. A planet is a HUGE thing, Reach even more so because it is almost TWICE the size of Earth. A planet is simply too big to control fully, and there will always be some kind of holdouts and valuable salvage.
You play from the Covenant perspective, you've just been promoted to the Zealot team that we see at the start of Halo Reach, having taken the Sabre launch facility and forcing the UNSC to retreat from it after the events of Operation Uppercut. The main Covenant fleet appears over Reach and begins crushing the UNSC at almost every turn. Your unit is assigned by Thel'Vadam (the future Arbiter) to destroy the facility powering Reach's orbital defense grid. You show up, proceed to murder the UNSC garrisoned there, deactivate the generators and move on to a new offensive in the city of New Alexandria. You'd be part of the team that tracks Kat, Emile, Jun and Carter through the ground battle for the city, possibly even using a Scarab to attack a Scarab that Noble Team has hijacked on the way to the ONI tower. After that particular chaos your team loses track of Noble Team, and ends up pinning a squad of ODST down inside a tower while the UNSC is pulling out of the city. You get a glimpse of a Spartan-III in a Falcon that allows the ODSTs to escape and you track it back to the ONI tower and discover where Noble Team was holed up. You then mark it for glassing and quite possibly get to be the Elite that shoots Kat in the head and kill her.
After that, Thel Vadam orders you to assault the Pillar of Autumn, and you get to be flying or riding in one of the Bashees/Phantoms that Emile takes out at the start of the mission. You then spend most of the level racing towards the Pillar of Autumn, finding another Phantom and getting there right as Noble 6 delivers the Package to Keyes. You are either the fuel-rod cannon Zealot that tries to murder Noble Six as he makes his way to the Mass Driver after Emile is killed, or you get to be the Elite that kills Emile, you suffering near fatal wounds in the process and the last thing you see before you lose consciousness is Noble 6 taking down the cruiser with the Mass Driver.
When you wake up, Thel Vadam tells you that the humans have been utterly crushed, but the Pillar of Autumn got away. Having failed your mission, your squad dead, you're demoted to to Major and you're being assigned to janitor duty: told to go clear out human stragglers in other locations around Reach (all of which are blown to hell and back by the fighting).
Eventually you'd start following the trail of Jun and Halsey, possible uncovering more and more Forerunner things that help cleanse the shame from your name. After each mission you'd climb back up towards Zealot rank, and would be able to customize your armor and at least your ability load with active camo, jump-pack, etc.
Eventually you'd get back to back to Zealot and one of the really big missions of the game would be breaking into Menachite Mountain, chasing after RedTeam, Halsey and eventually leading a massive Covenant assault force against the humans in the Artifact Chamber that we read about in the First Strike novel, to keep the humans from stealing the Forerunner Artifact. I'd imagine that this mission would be highly focused on really showing off how absolutely deadly the Spartans-IIs are, and would probably be less massive battle and more of a hit and run engagement with you fighting each member or Red Team before you force them to retreat further back. This would continue until the Master Chief shows up and saves them all, leading to the final battle in Slipspace after the Ascendant-Justice/Gettysburg transitions to the weird Slipspace bubble created by the Forerunner Artifact that Red Team stole.
You'd get to kill several of the Spartan-IIs that die in the book before you're forced inside the A-J/Gettysburg as Cortana manages to fix the Slipspace problem. I would imagine that the final mission would take place either on the Unyielding Hierophant (the Covenant fleet station) and either fight the Spartan-II team that boards it, and after they escape, you lead the final charge to the now detached Ascendant Justice and get to be the Elite that stabs the UNSC admiral that had escaped Reach with the Spartans-IIs right before the A-J's reactors go critical and destroy the entire station and most of the Covenant fleet.
Then we could jump to the cutscene of the Prophet of Regret saying something along the lines of "Despite all of his failures, he has delivered to us a great gift..." And then you see Regret's fleet making the Slipspace jump to Earth, thus leading us into Halo 2.
And maybe, just maybe, in a post credits sequence, we see you floating a emergency lifeboat, a tiny, cramped thing, almost dead, when you get rescued by a Covenant ship.
Full of Brutes. All of which have orders to kill every Elite they find. You activate your plasma sword and the screen goes black.
Anyway, there is my idea on how to make a second Reach game. Build upon existing lore, give us another game playing as the Covenant, and help fill in how the Master chief got back to Earth after Halo 1 (though this is explained in First Strike, it is never fully explained in-game other than 'that's classified'. We get to see more of Reach (including the cut ground battle of New Alexandria) and we get some customization options. Possibly even some small scale squad commands (nothing too fancy) as you re-earned your Zealot rank. I think that, while however impossible and unlikely that this game would ever be made, it would really serve to tighten up not just the Expanded Universe stuff, but the actual Reach campaign itself.
Anyway, those are my thoughts.