^Very symbolic. Humanity and her colonies would not join the covenant the galaxie's U.N or like the roman empire. They team up with another rebellious race the Elites after both realizing the covenant is false and all it got was technology from the forerunners the ancestors of humanity. The covenant try to activate their Halos to jumpstart them on the great journey thinking it will give them spiritual evolution and bring them to the promised land back to the forerunner "Gods". By doing this they release the Flood a parisitical species controlled by the gravemind similar to the Borg from startrek.The gravemind trys to rape cortana in Halo 3 because she downloaded the Forerunner knowledge in Halo 1 and outlived her necessity to become more of an oracle for the Chief. Humanity fights the covenant to stop the Halos from bieng activated and destroying all life and after finally defeating them activate a Halo ring anyways to destroy the flood.
So after Halo 3 the covenant is disbanded and bieng punished, humanity can finally rebuild and the gravemind is destroyed essentially destroying the flood like cutting the head off a lion.
So much was going on in the galaxy and you only saw it from the Chief so I agree. Halo 3 ended everything perfectly left no undone ties and the chief lost in space a perfect closure.
I think that's why Halo 4 will be good its my assumption that they will divulge more of the universe like the forerunners and such. With all conflict out of the way I'm hoping they don't introduce a new threat and instead reveal humanities destiny with the forerunners.
The whole deal of the new trilogy is supposed to be Chief finding out his true destiny, and him being a demigod warrior hellbent and designed for nothing but war this should be good.