Assuming Ben won't die from the gunshot wound, he is now ready to join the Hostiles. Alpert told Ben he had to be patient. By this he means "We want to make sure you are special enough to join our group." I think the Island will heal Ben while Alpert and the Hostiles take notice, thus making Ben ready for his official conversion to a Hostile. A nice parallel would be John Locke being able to walk again which certainly got the Hostiles excited. From now until the Purge, Ben will be a spy for the Hostiles until the shift of power to the Hostiles after Dharma is eliminated.

Not a huge theory, of course, but I'd like to hear your responses whether you agree or disagree.