The first known Project Predacon was during the Great War. Megatron had Shockwave clone a small batch that was sent to Earth to guard the large amounts of Energon reserves and kill any Autobots. After doing so, the Predacons waited for Megatron, becoming part of human mythology and eventually died. When Megatron came to Earth, he discovered the Predacons were all dead. With Shockwave, believed to be offline, the fossils were abandoned and powerful Decepticons, such as Skyquake, were left to guard the Energon.
Shockwave had in fact survived and resumed work on Project Predacon. He cloned a new Predacon. Without any orders or need for the Predacon he resumed work on other projects. When he detected the Omega Lock's energy signature he went to investigate. He ended up rejoining the Decepticon ranks and learned they were hunting the scattered Autobots. He suggested using the Predacon he had cloned.
The Predacon was dispatched first to hunt down Wheeljack and second to kill the Autobot invaders. It failed in both tasks and was Ground Bridged to the Arctic by Ratchet. Despite this, Megatron revisited the project and collected the fossils from the first clone batch to create an army of "Beast Machine Super Soldiers". The first Predacon had by this time escaped its Arctic prison and returned to the Nemesis.
When the Predacon clones were three solar cycles from being combat worthy, the existing Predacon revealed that he had become intelligent enough to transform into his robot mode by studying the other Decepticons. Shockwave concluded that the previous Predacons never displayed the ability due to the lack of historical evidence proving if they had the ability.
The Predacon dubbed itself Predaking and asked for command of the other Predacons, all the while pledging loyalty. The Decepticons feared Predaking would teach the other Predacons to transform as well, then realize his small squadron possessed greater might than what remained of the Decepticons (due to Starscream and Knock Out's super soldier project) and would overthrow them.
Megatron concluded there was no other choice, but to kill the Predacon clones. Starscream came up with a plan to put the blame on the Autobots. The Predacon clones would be destroyed, and Predaking would destroy the Autobots or they him.
Shockwave confirmed no beast CNA survived the explosion. Project Predacon has since been scrapped. However, Project Predacon was brought back to life by Starscream and Shockwave. Two new Predacons had been cloned by Starscream and Shockwave, intended to be used in a new army against the Autobots. Bumblebee and a group of other Autobots travelled to the burial ground in search of answers involving two living Predacons, though Predaking turned them away. He later discovered they were right and attempted to draw in both Predacons with a fire signal, though it instead drew in a now-Unicron-possessed Megatron. He found the Predacon burial ground empty when he returned but successfully discovered the two living Predacons. Working together, they helped the Autobots save Cybertron from destruction.
Predaking and his new servants later closed in on Starscream at Darkmount, claiming to be there for some well-deserved revenge.
The explosion of Synth-En and Predacon CNA created Cyber Matter. This prompted the Decepticons to begin reconstruction of the Omega Lock.
When Ratchet was captured to try and stabalize the Synth-En, Knock Out let slip that the Autobots were allowed to destroy the Predacon clones. When he completed the formula, Ratchet was given to Predaking to be killed. Ratchet then said if Predaking was intelligent he should rise above his rage that Wheeljack and Magnus had murdered his brothers and analyze the enormity of the coincidence that the Autobots found the lab by chance. Ratchet told him Megatron ordered the destruction of the clones out of fear.
Predaking went on a rampage killing everything in sight. Megatron concluded the Dark Star Saber could stop him. On his way to the vault the two clashed. Predaking seemed to be winning until Starscream shot him in the back. This allowed Megatron to toss him out an airlock. He claimed Predaking would have won if he had "faced me as a beast!"
In the end, Project Predacon was vital in restoring Cybertron.