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A four-part story, part of BotCon's Reaching the Omega Point.
As the story gains time-travel aspects, the storytelling becomes more fractured, with points of view leaping from timeframe to timeframe. It makes far more sense to summarize all of these chapters as a whole than to go one-by-one.
We are introduced to the Covenant of Primus, a 12-member group of Transformers created by Primus before Cybertron. Their creation-myth follows the Marvel US comic, which states that there had once been a universe of god-like energy beings, of whom Unicron was one. He devoured that universe and all his fellow gods, then slumbered. But while he rested, a new universe exploded around him, and it created Primus as its protector. When Unicron awoke and began consuming again, Primus battled him. These battles led to Primus' fateful plan to trap himself and Unicron in asteroids. But - in an addition to the previously-revealed creation story - Primus made a "dry run" of his plan, cyberforming the moon Protos of a giant planet called Methuseluh. He populated Protos with the Covenant, whom he tasked with overseeing the fate of their robotic brethren yet to come.
And so, as Cybertron was created and the Transformers rose up, the Covenant observed from afar and quietly intervened when necessary to maintain Primus's Grand Plan. They were constantly on guard for an apocalypse called "Point Omega, or Shokaract, the battle that would decide the final fate of the Transformer race." They would occasionally receive warnings from a god called the Chronarchitect, such as when Unicron's 2005 attack on Cybertron loomed. And they received another sometime just before BW Megatron left for prehistoric Earth. It was on this warning that four of the Covenant time-traveled to various temporal hot-spots. Three returned empty-handed, but the fourth (Scorpius) hit paydirt in the far future of the 32nd century.
Calling himself "Sandstorm," he aligned himself with the Predacons and came to lead the resistance against an interplanetary warlord with the portentious name of Shokaract. Shokaract had once been a Predacon soldier himself, under the command of some Megatron or other and known simply as "the Hunter." It's unclear when this was, but at some point, the Hunter was on Earth, pursued by Maximals. He took refuge in a cave, where he made a grand discovery: The essence of Unicron.
For in this timeline, when Unicron appeared to have been destroyed in 2005, he had actually thrown his own essence back in time at the moment of his defeat. Somehow he ended up deep in a cave on prehistoric Earth, weakened and waiting for someone to discover him. Eons passed, but eventually salvation did come in the form of the Hunter, who took the "Dark Essence" and used its power to create an empire spanning the galaxy. Naming himself "Shokaract" and bearing the "Matrix of Conquest," his supremacy seemed secure. But for some reason, in the aforementioned 32nd century, he became worried about a "dimensional key" on Earth during the Beast Wars, a device that apparently was related to a "great unraveling, a disruption to the timeline that had to be righted."
He sends one of his top lieutenants (or "Heralds") back in time to retrieve the dimensional key. This agent is Antagony, and it becomes clear that the mysterious "artifact" from Visitations was the dimensional key. Moreover, the "shadowy figure" who got it first was its owner, Apelinq. It seems the device was his "transfer interlink," an uncannily powerful tool he uses for many purposes. This element of the plot will be covered later. Suffice it to say that Antagony failed, she was captured by Megatron, and rather than reveal her secrets to his brain-scan, she mind-wipes herself into vegetablehood.
So Shokaract begins preparing another Herald, Cataclysm, to discover Antagony's fate and check on the Dark Essence. When the resistance catches wind of this, desperate plans are hatched to stop him. One of the rebels, called simply "the Veteran" (probably an aged Swoop), captures Cataclysm's rejected and half-dead "fission-brother," who is called "the Cub." Sandstorm orders the Veteran to merge his spark with the Cub in order to gain whatever crucial information would get them inside Shokaract's base. The merger works, and the resulting Transformer called "Windrazor" makes for Shokaract's palace.
Simultaneously, Sandstorm takes a team in search of a strange quasi-reality called "J'nwan," reached through a maddening dimensional rift on Cybertron. Many of the Autobot and Decepticon heroes of old had retreated there after their war was finished, and he tries to enlist their aid in the coming apocalypse. However, his team gets destroyed passing through the rift, and his pleas to the legendary figures are rebuffed, so he returns empty-handed. Eventually, he decides that he must go back to the Beast Wars himself, a decision that's reflected by the rest of the Covenant, who independently choose to make the temporal trip as well.
Meanwhile, Windrazor's infiltration of Shokaract's fortress goes swimmingly, and he assaults Cataclysm just as the Herald is opening a transwarp portal to the Beast era. The two go tumbling through the vortex, and Windrazor manages to throw Cataclysm outside the temporal tunnel and into oblivion. Windrazor lands on prehistoric Earth, and his first sight is that of dragon Megatron rising from a volcano (presumably the last scene of "Master Blaster"). Windrazor also discovers that Cataclysm's destruction wasn't quite complete: A tracking device also survived the trip. He uses it to search for the Dark Essence, all the while unknowingly followed by the Beast Warriors (who had detected his arrival). While battles erupt behind him, he finds the fateful cave and the Dark Essence within. Unicron possesses Windrazor, and the combined being attacks the Beast Warriors. But when the Veteran and the Cub team up to resist the evil influence, they exorcise themselves of the Essence, which retreats back to its cave.
Then Shokaract arrives.