Gentlemen, When we visit the wastes of Boston and New York, Who here will wander the wastes under our flag, and resurrect a once-great nation?

Today, a few elderly Enclave survivors make an existence on the fringe of NCR territories, keeping their heads down for fear of persecution. Many left for the Mojave Wasteland, where the NCR's grip was weaker due to the presence of Caesar's Legion. Enclave Remnants may have supported the Courier at the Second Battle of Hoover Dam, desperate for a final shot at glory, but whether they joined the Courier and the outcome of the battle is unknown.
Before the destruction of the East Coast Enclave, the engineers at Adams AFB sent a reinforced eyebot, ED-E, to Navarro to be serviced there, apparently unaware of the destruction of the outpost some forty years prior. ED-E's programming contains a message saying that any repairs needed on the way were to be made by Chicago Enclave personnel, indicating that there may be outposts there. The Illinois license plate bolted to ED-E's side also seems to support the idea that such Enclave outposts still exist elsewhere in North America, but also that their resources may be very limited (or that at least one Enclave technician has a strange sense of humor).

After the destruction of Raven Rock, the Enclave performed a mixture of tactical retreat and all-out flight, and their grip on the Capital Wasteland loosened severely. Now contending with malcontented soldiers, the remains of Enclave Camps dotted throughout the Wasteland with little or no contact or on-going tactical orders, and a lack of new recruits, the Enclave may be a doomed force. However, a small influx of specially trained fighters is seeking to fill the gap left by the Brotherhood of Steel advances. Posted to previously unknown and highly secretive locations outside of the Capital Wasteland, only the most veteran of Enclave forces trained in multiple forms of combat earn the right to call themselves Sigma. These six-person squads featured a leader clad in Hellfire Armor and carrying heavy incinerators, and each member had seen numerous combat stories and lived to tell about them. Sigma Squads were posted around locations deemed by Enclave high command as “imperative” to the salvation of the cause.

When, in 2277, Project Purity was completed, the Enclave acted at once. Troops under Autumn occupied the Purifier, and established a presence in the wastes, which was resisted by the Brotherhood of Steel. After retrieving a Garden of Eden Creation Kit from Vault 87, Eden attempted to recruit the individual known as the Lone Wanderer to work as a double agent, participating in the Brotherhood's attempted reclamation of Project Purity but infecting the water supply with the modified FEV at the last moment. The Lone Wanderer took the modified FEV, and exploited the fact that Eden was actually a sentient ZAX supercomputer to convince Eden to shut down and initiate Raven Rock's self-destruct sequence (If chosen).
Eden was opposed by Colonel Autumn, who wanted to make a bid to lead the populace by completing and activating the purifier, thus providing the Enclave with a strong bargaining chip in unifying the wastes under their flag. When the Brotherhood took the Jefferson Memorial, Autumn was defeated by the Lone Wanderer, but it is not known whether he survived. The Lone Wanderer stood poised to finally realize the Enclave's goal of purifying the wasteland, but it is unknown to history whether or not they took that action.

Later on, the Adams Air Force Base was destroyed by the Brotherhood. The Enclave were permanently fractured, and were reduced to small remnants.

In D.C., the ZAX mainframe installed in Raven Rock to ensure continuity-of-government continued to function until the destruction of the oil rig. When President Richardson was vaporized, ZAX created a persona, John Henry Eden to claim the post and assume authority over the remaining California Enclave forces, in addition to resuming construction of military ordnance to provide for the resource-stricken subordinates. Augustus Autumn was chosen as the commander of the armed forces (succeeding his father). A series of eyebots was sent to roam the Wasteland, spreading hope. Eden could spout his pro-government rhetoric, and promise a return of the pre-War America of legend: a land of white picket fences, baseball, apple pie, and good, old-fashioned American global supremacy.
President Eden’s secretive plan all along has been to rule over an America of the “pure,” free from any mutation. He has learned of a ridiculously ambitious experiment known as Project Purity, and knew the time to strike had come: His Enclave forces would “reclaim” the Jefferson Memorial. By controlling the purified water, Eden would control the Capital Wasteland, and the rest of the country eventually. What better way to administer modified F.E.V.— which kills anyone infected with any form of mutation—than through a deceptively clean water supply?