The Everfree Conflict was a major battle that took place in the Equestrian Wasteland, around the ruins of Everfree City containing Everfree Town.

The battle was an attempt by five major factions (the New Canterlot Republic, the Brotherhood of Steel, the Equestrian Institute of Science and Technology, the Grand Pegasus Enclave, and Caesar's Legion) to conquer and control Everfree Town in order to access the secrets and hordes of weaponry located beneath the ruins in massive storage bunkers. While each faction had their own agenda for the town that sat atop this throne of armaments, they all prioritised the weapons over the people.

The first side to attempt a strike at Everfree was the Legion coming from the South. However they were surprised to find that the town was under the protection of the Lunar Militia, a small band of warriors from the town, and was even being defended by a few of the famous names in the Wasteland including the Psionic Storm (Union Strike), the Pilot (Scootaloo), the Titan (Sevens), the Revenant (Fielde Locke) and the Sheriff (Apple Bramley). They also discovered one of their own, the famed Legate Aelius, had abandoned the Legion and was defending the town. Paladin Trasque of the Brotherhood of Steel and Sergeant Jones of the NCR also abandoned their factions to protect the town.

The defenders managed to hold the Legion at bay, but the NCR arrived from the North. This divided the defensive fronts of the town, making it harder to protect, but they continued to hold their home. As time went on, the Brotherhood arrived from the East, the Enclave from the North-East, and the Institute from the South-East in their plight to seize the Pre-War treasures stashed below the ruined city. The fight continued as none of the factions could pierce the defences of the Lunar Militia, who were considered the underdogs of the fight.

The factions began to fight one-another, mainly the massive conflicts between the NCR, BoS, Enclave, and Institute, as the attempts got more and more desperate. Eventually the Enclave summoned their mighty flying fortresses known as the Thunderhead Carriers to take the city, but were interrupted by the Brotherhood's own carrier ships. As the Institute did not wish to be outdone, they deployed their own ships via teleportation. This leads to an accident in which an Institute ship teleports into the exact location a Brotherhood ship currently is, causing a massive molecular rupture and destroying the two ships in a massive fireball and shockwave strong enough to cause a few of the ruined skyscrapers in Everfree City to collapse. The NCR and Legion, not having ships of their own, began to wear down their ground forces.

Eventually the Legion was utterly defeated and what little remained of their forces fled back to the Southern areas known as the Glowing Sea. Few of their battered forces survived the trip back to Fort Glory as they either died from injuries/radiation poisoning or were picked off by opportunistic Raiders and mutated creatures located in the Glowing Sea and the surrounding areas. Those that did survived found their camp completely void of life, learning that in their absence the town had been attacked by a mutated Alicorn and Caesar had been killed along with his Frumentarii, leaving the demoralised soldiers with no leaders as all of the other Legates had been slain by Aelius. News caught on and Caesar's Legion was soon declared dead by all settlements, what little of their remaining ranks vanishing into the Glowing Sea.

The New Canterlot Republic ordered a full retreat despite their apparent control of the situations erupting in their areas. This was mostly due to General Lee Oliver's assumptions that the other three major factions would utterly destroy one-another as well as the city, leaving easy pickings for later NCR forces. However during the retreat, NCR forces were split in two by a crashing Enclave Thunderhead, leaving many soldiers isolated between the blazing wreck of a Thunderhead and the Lunar Militia. The surviving forces began losing areas outside of their home territory, eventually leaving the NCR with only Canterlot and New Pegasus under their control, both cities cut off by Raiders, mutants, and now the Lunar Militia.

The Equestrian Institute of Science and Technology eventually issued a tactical withdrawal, and began teleporting it's forces out of the city limits and having their ships transported to a save haven below the ground to the South-East. Remaining Synths were wiped away by the Lunar Militia, Brotherhood of Steel, and Grand Pegasus Enclave.

Eventually the Enclave and Brotherhood both initiated retreat orders, with their carriers still engaging in combat even during the retreat. This led to a Brotherhood ship attempting to flee being shot down by the Enclave's capital ship (housing President John Henry Eden) only to uncontrollably veer towards its attacker as it exploded, destroying the Enclave ship and Eden in the process. With their leader dead, the Enclave was forced to retreat back to their aquatic base (Innovation) and gather their forces for a possible counterattack. However their new leaders, General Autumn Leaf and General Firestorm, were divided and their quarrels caused the downfall of the Enclave entirely within only 2 years.

The Brotherhood retreated to their home in Horseshoe Bay, but not until after their leaders (Elder Pakai, Elder Maxson, Elder McNamara, and Elder Basalt) were killed. Only one eligible leader, the daughter of Elder Basalt (Thyme), was ever promoted to Elder, but the young child was not ready for such a position and though it remained a strong fighting force, the Brotherhood was unable to hold any land in the Wasteland.

The Lunar Militia, as the last team standing in Everfree Town, declared themselves victorious. Not long afterwards, they began salvaging the technologies and weapons left behind by their foes during their panicked retreats, becoming a well-known faction in the Wasteland known as the Lunar Settlement Defence Alliance. As words of their victory spread, their numbers grew exponentially overnight. Before long, the militia had turned into a massive army with the most advanced weaponry in their possession. Once the storage bunkers below Everfree Ruins were opened, they became almost unbeatable with their technology and units becoming the most advanced known.

This battle led to the heroes that helped Everfree Town parting ways to pursue their original goals, thinking they had just saved the Wastes by creating this new army that would defend settlements from the tyrannical factions that had survived the fight. However, they were wrong.

Instead, the LSDA was disbanded, and in its place the New Lunar Order rose to seize ultimate power in the Wasteland, as if the Midnight of the past had been reborn.