Haven was built by the Fire Ant race for the use of the fledgling Brotherhood. The first Guardian brought there was Steppenwolf, shortly after the death of his father Edmund. For an unknown amount of time, he trained under Christopheles in physical, mental, and mystical fields until he emerged as a full warrior Guardian. Once he defeated the Dark Legion for the first time, Haven became his base of operations. As time passed, he was joined by his descendants Moonwatcher, Harlan, and finally Rembrandt before the tragic death of Aaron. When Aaron's younger brother Jordan began training as a Guardian, it was decided that Haven's existence would be kept secret from the youngest Guardian until such time as he was ready to make his own journey there. To ensure this, the Brotherhood instituted a rather cold-hearted rite of passage in which the parent Guardian would leave their nine-year-old successor on Angel Island and walk through what appeared to be a wall of fire but was actually a hologram concealing a portal to Haven. The younger Guardian would be left under the impression that their parent was dead, and wouldn't be persuaded otherwise until years later.
In this fashion, the Brotherhood maintained their hidden vigil over Mobius, keeping this same system in place up until the time of Knuckles. Unfortunately, though Haven's security was tight, one enemy managed to slip through: Moritori Rex, a Dark Legion Grandmaster who gained entrance by impersonating a wounded Tobor. Aside from that, the only non-Guardians to take up residence in Haven were Alicia Acorn and her son Elias, who crash-landed on Angel Island while fleeing the Kingdom of Acorn for safety. While Alicia remained in stasis for years, Elias was brought up by the Brotherhood until he became old enough to explore Angel Island.
After making his own journey to Haven, Locke would monitor his son Knuckles and his allies the Chaotix secretly over many years. He would intervene several times, first with the rest of the Brotherhood to put a halt to Knuckles being bullied by Monk by throwing the ape off the island. Later, he would step in to stop Enerjak from defeating Knuckles during their first battle by sending him into outer space. The Brotherhood would continue to monitor events as the Dark Legion made their permanent return to Mobius after the Ultimate Annihilator created by Dr. Ivo Robotnik went off, and later as Echidnaopolis was also restored. Sabre, Locke's father, would join him in his vigil, and soon both watched the unfolding horror as Enerjak returned to Angel Island, capturing the Chaotix, Archimedes and Deo Volente the Fire Ants, and almost killing Knuckles.
When Mammoth Mogul, transformed into the more powerful Master Mogul, attempted to take control of Angel Island's remaining two Chaos Emeralds to seize victory in his battle against Hyper Knuckles, Super Sonic, and Turbo Tails, the pair of them joined forces to use their link to the Emerald against him, helping bring about his sealing inside the newly created Master Emerald.
When Knuckles was taken from Angel Island by Athair, the only Guardian to deliberately leave the organization, the Brotherhood congregated at Haven to discuss Knuckles' rapidly developing powers. Amongst those gathered besides Locke and Sabre were Spectre, Thunderhawk, Sojourner, and Moritori in his Tobor guise. They argued over the situation with Knuckles, which soon turned into an argument over the policy of the Brotherhood itself. Semper Fidelis, Archimedes father and one of three Fire Ants present at that meeting, summed up the Brotherhood's choices: they could either allow the Echidnas to become irrelevant to Mobius' future, or they could lead them into a new golden age.
In any event, no solution was reached before the true Tobor returned to Angel Island, inciting the Brotherhood's curiosity before disappearing into the Twilight Zone with Kragok of the Dark Legion. Not long afterwards, Knuckles walked into the Haven portal seeking answers, appearing in Haven many years ahead of schedule. As the Brotherhood accepted the situation, Knuckles helped them uncover Moritori's deception, and he escape before they could catch him, leaving a warning that they would all be killed. The Royal Secret Service came to Angel Island looking for the missing members of the Acorn Kingdom's royal family at about this time, and the Brotherhood turned their charges over to them.
Knuckles would later be brought back to Haven at the Brotherhood's behest by Locke, who explained to him the past that had led to his mutation into the most powerful Guardian ever born. Just prior to this, the Brotherhood were watching as the Dark Legion attempted to gain control of Echidnaopolis through politics, only to fail as their android political candidate, Benedict, was taken out by an EMP generated by Knuckles. Haven itself fell to them during this, but the escape of Locke and Spectre and their subsequent ambush of Moritori and his granddaughter, Lien-Da, would enable them to retake the facility and free their family members.
They would then host Princess Sally Acorn, who came seeking an alliance between her Kingdom and the Echidnas against Dr. Eggman. Though the Brotherhood were willing, one of their conditions-that the Kingdom agree to the use of munitions-was unacceptable to Sally, who then felt betrayed as Knuckles did nothing to convince the Brotherhood to help anyway. The Brotherhood took Hunter prisoner after Knuckles defeated him.
Haven and the Brotherhood were soon faced with the return of the Dark Legion. Led by their most senior member, Mathias, they launched an attack on the Legion-controlled Grand Conservatory, only to be caught up by the Quantum Beam. Haven was destroyed prior to their return, leading to the construction of a new base called Haven II.