From Halopedia, the Halo wiki
Play the mission on Easy difficulty with the Catch, Sugar Cookies, Pain Train, Bountiful Harvest and Emperor Skulls active.
Send a pair of Gauss Warthogs to each of the colonies and kill them to put them into hibernation.
Do this for each of the colonies. They respawn in 4 minutes.
You can choose to lock down a cobra outside each colony to permanantly weaken the Proto Gravemind and have time to build an army to defeat it.