The Covenant of Primus is best known as the name of the "holy text" of Transformers, their equivalent of the Bible, written in a manner similar to the Book of Revelation. Like that Earth text, it serves as something of a prophecy of what is to come in Cybertronian future—after perusing what he would later call "the good parts," a renegade Predacon gave himself the name "Megatron," taking it from a great destroyer that the book foretold the coming of. Although it resembles a book, the brief view of its "pages" that we are offered suggests that it is a recording device that holds the information electronically, rather than being made of paper. In an ironic twist, the events foretold in the Covenant were the same ones that were played out in the Beast Wars, with Megatron being that same great destroyer he took his name from.
A second Covenant of Primus exists, but rather than being a record it is an organization. According to the Botcon comics, the Covenant were the first 13 Transformers created by Primus. They were created in preparation for Point Omega, the foretold final battle against the evil Unicron. The Covenant were also created as a test by Primus, to assure that he would be able to manipulate the planetoid he was to become imprisoned in, and also as prototypes of the first Transformer race.
There are only two copies of the Covenant in existence. One was kept aboard the legendary Autobot spacecraft The Ark, while the second was stolen from its holding place on Cybertron by the Predacon secret police agent, Tarantulas and brought with him when he and the other members of Megatron and Optimus Primal's crews were blasted back in time and fought the Beast Wars on prehistoric Earth.
As the Beast Wars began to move towards their conclusion, Optimus Primal and Megatron reviewed the Covenant, for parallels between the book and reality made it seem like Primus had prophesized the Beast Wars. Optimus Primal recited datatrack 7.613, comparing its description of a warrior from the sky and the casting out of the dragon to the recent arrival of Tigerhawk and Megatron's loss of his base. Not long after, Megatron discovered and reactivated the crashed Decepticon spaceship, the Nemesis, comparing its rise from the ocean to the covenant's account of a great mountain emerging. In his glee, he recited the track that spoke of the destroyer, Megatron, and prophecy and history came together as it was finally understood that he was the Megatron the Covenant spoke of.
Uncovering the Ark, which the Maximals were using as their base, in accordance with another line from the Covenant, Megatron was confronted by Optimus Primal, the "great hero" the book foretold—but alas, as the book also said, he did not prevail. Though, as Optimus pointed out, he would not surrender either. Instead, as the Covenant predicted, "the spark of an enemy" held the key to victory, as the clone of Dinobot turned on Megatron and ensured his defeat and capture at the hands of the Maximals.
Hidden on the moon known as Protos, the Covenant-consisting of Leonicus, Aquator, Libras, Scorpius, Capricun, and several others, all based on the Greek Zodiac-waited. They had been created in preparation for a time when Unicron's evil would threaten all things, and when there would be no Autobot Matrix of Leadership to oppose him. They had one close call in the Earth year 2005, when Unicron attacked Cybertron. However, they were forced to wait again, as Unicron was brought down by Rodimus Prime.
For countless millennia they waited, watching as Cybertronian culture developed. At some unspecified point in time, they were met by the Chronarchitect, an ancient time traveler and kin to Primus and Unicron. He warned them of the coming Point Omega, and they began preparations. During this period, Scorpius disappeared, secretly travelling to Cybertron and taking up the identity Sandstorm, leader of the Maximal-Predacon resistance to the evil Shokaract. Sandstorm took several steps to prepare for Point Omega, which he knew was related to his efforts: in ancient Cybertronian, Point Omega translates into Shokaract, and the evil monarch carried the Dark Essence of Unicron within him.
Finally, after their long solace, the Covenant engaged in Point Omega. Taking place on prehistoric Earth, the battle was indeed against Shokaract, seeking to preserve his timeline by preventing Unicron's essence from seeping back into the timestream as it was in danger of doing. Assisted by Optimus Primal's crew of Maximals, the Wrecker Apelinq, the hybrid Windrazor, and the legends of Cybertron, the Covenant fought against their nemesis. Unfortunately, the battle was grossly one-sided, as Shokaract's power made it impossible for the assembled forces to defeat him.
Scorpius, realizing what had to be done, moved in on Shokaract. The evil Transformer did not attack him, as Scorpius had evidently masqueraded as one of Shokaract's Heralds. However, the illusion was shattered as Scorpius struck Shokaract with his essence, the pure energy from Primus' own life force. Shokaract's protective cloak of dark energy was broken, and in his fury he destroyed Scorpius. The brave warrior's sacrifice was not in vain, as the rest of the Covenant pooled their energies to access the Decepticon Matrix of Conquest, which carried Unicron's energy. Forming an entity duplicate of Primus, they engaged a similar duplicate of Unicron.
The remaining combatants, seeing their opportunity, fired upon Shokaract. The massive Predacon fell under the firepower of countless Cybertronians, including such legendary figures as Megatron and Optimus Prime. Meanwhile, the Covenant shattered the link between Shokaract's Dark Essence and the one he sought to keep from slipping into the timestream, causing the latter to disappear. Shokaract's corrupted timeline was erased, and the Covenant vanished, their purpose fulfilled.
From a promo, there is a section that says:
"And it was written in the Covenant of Primus that when the 47 Spheres align a perpetual conflict will culminate upon a world forged from chaos and the weak shall perish in the shadow of a rising darkness."