both of them are missing, and SoF was never found and in the legendary ending the captain is woken up by serina who said and i quote “captain wake up, somethings happened” so anything could have happened sending them to the ark but here is my general idea of how things go.
chief lands on the strange planet and wakes up and he and cortona scout the area discovering the flood have infested the planet, they fight them off and use a warthog from the “forward unto dawn” to travel to a location where cortana picks up a faint signal. they go there and it turns out the signal is from spirit of fire in space and cortana jumps into the signal and wakes up spirit of fire who say they went through a black hole and went back into cryo sleep(or something) cortana convinces them to go to the ground and as master chief gets cornered by the flood the three spartans show up and save him and chief gets emotional after thinking they were dead(lol) they go back to spirit of fire and catch the whole crew up on what has happened and serena and cortana exchange data on halo and the shield world and piece some of the puzzle together. the spirit goes into orbit and goes into the center of the planet and it turns out that was a shield world as well, they find a covenant ship inside though from the battle for the ark and see that some covenant and a minor prophet have found how to activate the forunner ships and they are prepareing to go to earth and wipe out humanity. the marines and spartans go down and begin to engage the covenant and fight off some of the flood that is trying to controll the ships as well(like in halo legends originsI) and chief finds that gravemind has come back after part of his knowledge escaped in a flood spore that melded with the ones on the shield world. they fight them off with vehicals from SoF and destroy the covenant as well and begin to fight the new gravemind and the rest of the flood, they win (yay!) they go back to the controll pad and shoot the last flood spore and the shield world shakes and a forunner voice says something and cortana translates it into “area is clear of flood. begin return procces” a stairway apears bellow them and they go in and find a portal where forunners are comeing in from and they introduce themselves to the spartans and master chief useing translation equipment. they explain that they hid away while the flood were on the shield world inside another dimension where all they do is exist and think, and they couldn’t fight the flood so they couldn’t come out. but they say their is a greater threat besides the flood. the crew of SoF get on a forunner ship while the rest of the forruners take they others and they set on a course for earth and the game ends. in the legendary ending the ships aproach earth and master chief uses his call sign 'sierra 117" to contact earth, he than gets on with lord hood and he says they have a lot to talk about.
also without spirit of fire where would master chief get guns and ammo from? because he’s on the edge of the galaxy spirit of fire is the most probable explenation to where he would get help. and forward unto dawn would not have that much on it and i also cant see them haveing a halo game with MC as the only human
if i worked for 343i right now this is defeniately what i would do for a game sequal to halo 3. but the main reason i posted this is to get the idea master chief finds the spirit of fire in everybodys head, and to prove that a sequal could work. thoughts?