Hi Heidi!
It is possible that your son is suffering with Migraine disease. The only way to find out for sure is to see a doctor for a proper diagnosis. Nobody can diagnose over the internet.
The fact that you mentioni your son was in and out of consciousness makes me wonder if it is something other than Migraine. What did the ER tell you after you were seen? Did they seem to think it could be Migraine?
Here are some links if you would like to read about Migraine disease. Your best bet would be to take your son to a neurologist first for a proper diagnosis.
Types of Migraines and headaches
Migraines: Where to Start
Good luck!