Ahh it's you. Been a while hasn't it? We WILL finish this.
Just you wait.
Not very different. Lets say Emile destroyed the phantom with the zealots in it, and any other ships and successfully blew up the cruiser. And six gets inside the autumn and is in halo CE.The game would have followed it's normal course with Noble Six being at Alpha Base with the ODST's or attending to other missions/recon.
He would have died with the ODST's in the Truth and Reconciliation unless he joined the Chief to destroy the POA.
Why wouldnt he fight with the chief? Because Keyes would've decided that the missions to get back the autumn would've guaranteed success. Then again if he and chief decided to blow up the autumn together, they would've made it. And six in halo 2 and halo 3 would be -blam!- awesome.