The Enclave do not exist anywhere outside of the United States. The Enclave from Fallout 3 were what was left of the Enclave at Navarro. Navarro was the only mainland base the Enclave established. The Enclave only existed on Control Station Enclave Oil Rig from the Great War to the events of Fallout 2.
The Enclave feared they would be contaminated if they went to the mainland. So they stayed on the rig. They only established Navarro so they could gather the resources they needed for their "kill everyone" plan which was the FEV Curling-13 virus. The Chosen One in Fallout 2 destroyed the Oil Rig. Leaving Navarro.
The Enclave from Navarro then split up. The Bulk of the Enclave went to Raven Rock in DC. The rest stayed at Navarro. Navarro later fell to the NCR. Raven Rock fell to the Lyons and his people. AAFB also fell. Thus the end of the Enclave.
There is a possibility that some still exist in an Outpost(s) in Chicago. But they would be remnants of remnants of remnants by now. Left behind in Chicago to act as a relay between Raven Rock and Navarro, which Ed-E and his travels would suggest.
The Enclave would/should be pretty destroyed by now. Fallout 3 was their last kick of the can so to speak.