In fallout 3 my first time playing it I was suppose to find information about my father at MegaTon. Well, I decided to blow up MegaTon instead. (via that one guy from Tempenny Tower). Where do I go after I blow up MegaTon to continue with the main quest of the game(finding my father)?
You can still follow the entire main quest without skipping anything but the Megaton parts.
You'll have to go to Galaxy News Radio and talk to Three Dog. More information about that can be found on the Fallout Wikia.
You have to visit Rivet City. Talk to Miss Li (she's a doctor) in the lab. Don't forget to pick up the "Vault doll" on her table ;)