I have a crazy idea, let's play Halo 2 and see where the story goes before we decide if there will be a Halo 3 or not. Saying absolutely not is like saying Star Wars would absolutely not have a third movie after Empire Strikes Back because everything was tapped. Obviously from watching Empire there was no way in hell that there couldn't be another Star Wars movie. It was begging for Jedi to wrap it all up.
Halo could be the same way. Don't believe me? Here's a three game storyline that would knock you on your @sses:
Halo 1: Well, we know this one.
Halo 2: MC returns to Earth where the Covs are attacking. After landing and fighting the covs a bit, he discovers that Earth is a nexus of Forerunner technology and has some sort of connection to a much more sinister and evil plot to scrouge our galaxy of all life (ala their Flood in H1.) The Covenant have been trying to stop this plan from happening, we just happened to get in their way. Cortana is actually an evil agent AI for this Forerunner plan and she manuveured the Pillar of Autumn into landing on the original Halo in order to remove a malfunctioning other AI (343 Guilty Spark.) Her mission complete and the needed information/materials (flood) retreived from Halo, she brings MC back to Earth to complete the plan. She opens a gate to another dimension and the Forerunners (or their servants) arrive and begin genociding Earth. The Covenant reveal that they have their own AI lifted from ancient technology that has driving them on the last few decades. Earth, MC, and the Covs team up to close this hole, end the war, and save themselves. MC kills Cortana (or sends her back) and the galaxy is saved.
Halo 3: After a period of peace and understanding, the Cov/Earth alliance learns that the Fores are going to launch a new overpowering assault. They decide to reopen the gate and take the fight to the Forerunners instead of waiting for death. They either convince MC to fight again or you are cast as a new "super" cyborg with all the best Cov/Earth tech. After being flung through the gate, the mission is a disaster and it is up to you (and the ancient AI) to shut the Forerunners down for good. Throughout the game you run across more and more technology that transforms MC into a super-being. You discover the Forerunners implanted humans on Earth to care for the eventual gate opening (after the flood) but that the plan had gone awry and humans lost their path. You face all the servants at their disposal and finally implode the Fore super weapon on themsleves (with the help of the last remaining Cov/Earth troops), wiping out their entire universe, all the Forerunners, and saving our universe in the process.
See, three games no problem...