Don't read on if you don't want spoilers.
I finished the game today. Story-wise, I don't know what to think. I wasn't really satisfied or convinced that everything got wrapped up in this game. At the end of the game, Cortana and Lord Hood acknowledge closure to the war with the Covenant and the fight against the Flood. It seems strange that just because the Prophet of Truth was killed that the Covenant is no more. I mean, all the Brutes left fighting didn't decide to just leave the fight, did they? What about all those Grunts and Jackals? And how is it that the Flood are gone just because they were destroyed on the Ark and on the new Halo ring? The Flood on those structures got there by way of High Charity. I find it hard to believe that there were no other Flood left anywhere else.
Arguably, because Truth was killed, the Covenant has no leader or voice left to carry on their delusional beliefs and give direction. And the Covenant supposedly glassed the area of Earth that the Flood occupied. Thus, my two gripes are possibly refuted. But it just felt like Bungie asked me to take a few leaps (or small jumps) of faith on some of the story elements. Suddenly the Covenant and Flood were "dead" and I felt like the Master Chief only solved a part of those problems.
As for the "mini cliffhanger" ending, who knows. I got the impression from this article that Bungie doesn't intend to focus on Halo again. That's just the conclusion I drew from that article, but others may feel differently. Aside from Halo Wars, if Bungie or Microsoft decides to use the Halo universe in a game story in the future, I doubt it could ever be as big as the Halo trilogy, and I hope they don't expect it to be. There shouldn't be a Halo 4: people are going to be bored with the same, continuing storyline, and do we really need another makeover of Halo multiplayer (ok, the multiplayer angle is a little off-topic). I'd be fine with another game that continue's the Master Chief's story, but I'd rather not see it under the Halo name.
So what is that blue light shining over the horizon of that dark planet at the end of Halo 3 (in the Legendary ending)? What is that dark planet? My only idea is that it's related to the "planet" Onyx in the Ghosts of Onyx novel, or that it's something else Forerunner-related. Which actually brings up another point - at the end of Ghosts of Onyx, Halsey and other Spartans were transported to another world of safety... did they end up at the Ark before it was destroyed? If so, did they get off of the Ark before it was destroyed? I sense a few additional Halo novels in the works....
What about other elements of Halo 3 besides the story? It was a blast to play. The environments were awesome and the battles were excellent. I actually enjoyed fighting those damn Brute packs. In H2, it was a grindfest to get through the damn game. In H3, it was more like "hell yeah" when you saw 8 Brutes waiting for you - and one of them had a BFH.
You know what I really missed though? Fighting against Elites. It was such a staple in H1 and H2. The n00b combo wasn't an effective tool this time around against the main enemy class.
Next, I'll be digging around Bnet and HBO to learn a little more about the story. Maybe some of the gaps that left me a little unsatisfied will be filled. And maybe some light will be shed on the ending...