This seemed like the best place to post this. It's a concept I've revisited a few times, based on the alternate BattleTech universe a friend of mine ran briefly WAY back in high school.
Author's Note: The major changes for this timeline do not start to affect until 3057, though the seeds are sown in early 3052.
After ComStar won the Battle of Tukayyid and a 15-year peace for the Inner Sphere, Precentor Martial Anastasius Focht knew the Successor States would not be ready for a renewed Clan invasion. With the splintering of the fanatic Word of Blake faction, ComStar had also lost much of its potential for uniting the Inner Sphere. Focht also feared (rightly) that the Successor States would squander their fifteen-year truce in yet more pointless infighting. A radical new solution would be required.
Focht had learned much about the Clans during his time with them, and now put that knowledge to work. He recreated the Clans breeding program, drawing from the genetic material of the best warriors in the Inner Sphere, resorting to subterfuge and even blackmail to attain particularly high-value samples. Fifteen years would be barely enough time to field a new generation of warrior who would, hopefully, be the equals of the Clans, when given the finest technology ComStar had to offer.
These artificially bred warriors, codenamed "BattleSphere," weren't just combined from genetic samples from promising Inner Sphere warriors. The Clans had spent generations of selective breeding perfecting their warriors, ComStar had no chance to catch up in only fifteen years. And so some of the most talented geneticists in the Inner Sphere were brought in to bring out the traits that would make these warriors the equal of the Clans. The Precentor Martial wanted the BattleSphere warriors to not just have superior reflexes and combat ability, he wanted them to be intelligent, independent thinkers that could still work together, with the drive and ambition to succeed in the face of hopeless odds, but with the clarity of thought to not throw their lives away in useless battles. One hundred warriors each were bread for fighting in BattleMechs, AeroSpace fighters, BattleArmor, and conventional vehicles. The BattleSphere warriors consistently outperformed their Inner Sphere counterparts, though they were not quite up to Clan standards yet. The Precentor Martial insisted they be trained on the best tech ComStar had to offer, and pushed for new innovations. With four hundred perfect warriors in perfect war machines, he could, perhaps, save the Inner Sphere.
Unfortunately, his fifteen-year-old warriors did not see the appeal in fighting and dying for a conglomeration of warring states that they had no loyalty and owed them nothing. On the eve of the expiration of the Tukayyid Truce in 3067, the BattleSphere warriors escaped ComStar custody, along with all the advanced equipment they could get their hands on and two dozen of ComStar's most promising young scientists. Having gambled everything on his ambitious BattleSphere plan, Focht had allowed plans by the Successor States to strike back at the Clans to languish. As a result, no one was wholly prepared for a renewed Clan invasion.
Meanwhile, Word of Blake spies in ComStar had heard of Focht's plan, and began to enact one of their own. At first experimenting with extreme cybernetic enhancement, the Blakists soon developed true AI and robots. Originally referred to in top-secret communiques as "machinas a deus" (machines from God), a mistranslation by several techs who spent less time on their Latin they should have resulted in them being referred to as "machina ex deus", eventually shorthanded to "Exos."
Word of Blake designed several different models of Exo body, or "platforms," into which individual Exo consciousness programs could be loaded. Some were covered in the same fake skin used in high-end cosmetic prosthetics, allowing them to blend in seamlessly with humans. Others were huge, easily able to beat out Clan Elementals in size and strength. Others were designed to most efficiently dispatch organic opponents using a terrifying array of on-board weaponry or their bare, cold, metal hands. All were built to roughly humanoid specification, allowing them access anywhere a human could go.
The idea of building 'Mechs, BattleArmor, and other vehicles to contain Exo "personalities" was only briefly discussed. Exo platforms were installed with high-capacity data transfer ports and plugged in, they could take over any electronic system as though it were their own bodies. Exo MechWarriors had no need of neurohelmets; simply "jacking in" to their 'Mech allowed them to move it as if it were a part of them. BattleArmor is, for all practical purposes, an Exo's second skin. An Exo AeroPilot can put its plane through any maneuver it can think of. Most startling of all, a single Exo can crew an entire combat vehicle with nothing but the power of its digital mind.
There is an old saying: raise no more demons than you can put down. Upon seeing the limitless potential of Exo platforms, the Word of Blake rushed them into mass production, creating two thousand individual units by 3067. As the Truce of Tukayyid expired, the Word of Blake turned their newest creations loose, and told them to exterminate the Clans once and for all.
But the Exos had other ideas.
For the first time since the first Exo had been activated with full self-awareness, the sapient machines found themselves installed in fully-functional war machines, all safeties and overrides removed. They turned their guns on the Clans. . . and anything else that wasn't Exo.
Before anyone could react, the Exos had carved a swath out of the Smoke Jaguar and Ghost Bear occupation zones, as well as the Draconis Combine and a chunk of the Free Worlds League, where they had been created. Inner Sphere and Clan forces both mobilized to stop this surprising new threat, but it seemed that the Exo 'Mechs grew more advanced by the day, soon outstripping even the technological superiority enjoyed by the Clans. Worse, the Exos had no sense of honor or fair play to be taken advantage of. The machines had only one directive. . . exterminate humanity.
As 3068 dawned, much of what had been the Inner Sphere had been conquered by the Exos, humans within their sphere of influence disposed of. In a last ditch effort, the Successor States invited all the Clans, regardless of Warden/Crusader or Home/Invader boundaries, to meet and prepare a massive, coordinated offensive against this enemy of humanity. By March of 3068, the single largest military force ever assembled, composed of units from every Successor State and every Clan, began to take back the Inner Sphere from the Exos. Even with all the combined military might arrayed against them, the Exos gave as good as they got, and the tide of war still might have turned against the Inner Sphere. . . until the BattleSphere returned.
The BattleSphere warriors had found a set of homeworlds for themselves, and immediately proceeded to increase their numbers through eugenics and cloning, using the knowledge of the captured ComStar scientists. While their first sibko was still being decanted, the BattleSphere had cloned enough warrior to assemble a sizeable fighting force. Keeping tabs on the Inner Sphere, paranoid that ComStar would come after them, the BattleSphere had seen the threat of the Exos spread, and would now take steps to obliterate it.
In a short span of time, the BattleSphere had updated their machines with highly experimental technology, raided from the work of ComStar and its spies in institutions such as NAIS. While none of it was battlefield ready, the bleeding edge innovations pioneered by the brilliant warriors and implemented by experienced ComStar techs proved to be just enough to combat the Exos' own technological quantum leap. Spearheaded by BattleSphere units, the Inner Sphere and Clan forces began to make serious headway in reclaiming territory from the Exos.
Then, on January 4th, 3069, the Exos vanished.
Overnight on besieged worlds, Exo forces fled defensive positions, pausing only long enough to totally destroy any technology they didn't take with them. Across the Exo occupation zone, the robotic enemy left, a retreat so perfectly executed it was almost as though they'd never been.
The BattleSphere again went their own way, developing their own homeworlds and their own society. The Clans retreated back to their occupation zones, licking wounds and stunned by the sudden appearance of the new enemy. In the face of the Exos, the Warden movement gained significant momentum, finally having an enemy of humanity to focus its arguments against. And the Successor States reclaimed their scorched worlds, began rebuilding their old civilizations, settling back into the familiar map lines that had existed for centuries. . .