I was just playing Mt. St. Helens (http://knucklecracker.com/creeperworld/mapcomments.php?page=&sort=&author=&id=160), a great looking map by the way. When I don't dismiss the failure dialog by clicking 'Continue', but instead unpause the game, it will keep running. You can do this for every survival pod and then energize the rift (although mission failure is still detected at the end screen).