I think you mean Dr. Gerald Robotnick, considering he's the owner of the ARK.
The human-Covenant war probably would have lasted about thirty seconds if Sonic, Shadow, and the seven Chaos Emeralds were on the UNSC's side.
Sonic devastated Eggman's fleet at the beginning of Unleashed, I'm sure he and Shadow wouldn't have too much trouble finding a way to eradicate the entire Covenant fleet, as well as High Charity.
343, MAKE DEAL WITH SEGA AND MAKE CROSSOVER GAME NAO.
[Edited on 01.18.2012 8:53 AM PST]