Its been a short time since optimus' team has returned to cybertron; megatron and his decepticons are locked up in their own former fortress of trypticon and primes group are heroes. On earth, starscream is brought back to life by another allspark fragment, thanks to slipstream, soundwave, and laserbeak. The regrouped Constructicons have repaired the lugnut supreme crashed on dinobot island, though it can't transform into robot mode, it is now a fully functional ship. Dirtboss has also created a new, more loyal constructicon, Skipjack, cloned from an autobots info originally stored in omega supreme. The decepticons highjack the ship and leave the constructicons still stranded on earth, with dirtboss resolving to bolster their ranks but are chased off by the dinobots.
On cybertron, there is a lot of arguing going on between sentinel, optimus and the autobot high council concerning the fate of the allspark matrix, the magnus hammer and leadership of the autobots. The council considers impeaching sentinel in favor of optimus and sentinel storms out. After sentinel runs into and has it out with jazz, he sneaks of to his private lab. He has been building a secret, powerful weapon to rally the autobots behind him and scare the council into making him permanent magnus and so he can take possession of the allspark and birth a new autobot army. Meanwhile the autobots from earth are dealing with all their own affairs, all the while being treated as heroes by the populace, but purposely separated from each other on sentinals orders . Each one handles things in their own way, as well as the loss of prowl. Sari is overwhelmed by it all; trying to learn about her origins and being judged by the other cybertronians. Optimus arranges a eulogy and cremation for prowl with a massive turn out for the fallen hero. Sari begins her cybertronian schooling under arcee and Kup
Within trypticon prison, megatron meditates on recent events and what lies before him. In space, on the lugnut supreme, they have picked up the wandering skywarp and thundercracker(all of the clones actually have their names now). Starscream wishes to go take control of the scattered decepticon legions, but is outnumbered when the others decide they will rescue megatron. In prison megatron tries to find a weakness in the prison, the other cons are little help. He is visited by optimus and the two have an exchange of quips and views, and even share an awkward moment of understanding before he must leave. He is later visited by sentinel, who informs megatron that his decepeticons are attacking autobot energon farms out of retaliation for his capture. sentinal bargains and offers him "perks" if he will advise on dealing with the situation. megatron does so, confident that sentinal will fail regard. One such perk is freedom from his cell, and though constantly restrained, he surveys his surrounding and, knowing the inner workings of trypticon, begins planning his grand escape.
Sentinals new Powermaster weapon is finished and he prepares to embrace his future. Also, confident in his position, he announces a public trial/execution of megatron. The omega supreme has arrived and is waiting around one of cybertron's moons. They send laserbeak to the planet and he eventually finds megatron, restrained in the prison court yard. Laserbeak lands on his shoulder then opens a radio link between starscream and him. the two then coordinate the escape plan. That night, laserbeak sabotages the prison alarms and disengages the laser cell doors. Starscrteam and his group infiltrate the prison, kill the guards then leads lugnut, shockwave, blitzwing, sunstorm, ramjet and a few others through the prison. Ramjet, sunstorm and many of the other prisoners scatter and lugnut recklessly heads for the elite guard HQ to free megatron while the others continue with the plan.
At the public trial Sentinel continues to push for megatrons immediate execution, optimus and others are less severe about it and megatrons political maneuvering continues to stir debate. Suddenly the trial is interrupted by the rumble of trypticon prison and the whole city of kaon erupting from the surface as a mobile base controlled by the decpeticons, which was megatrons grand scheme. Suddenly lugnut bursts in and frees megatron, but is blasted clear through by sentinel with his new powermaster weapon. Lugnut begs his master for help, but not wanting to risk his own life even for his most loyal servant, callously flies away, leaving lugnut stunned and hurt in his last moment of life. Megatron joins the cons on kaon, which speeds away from cybertron while destroying its planetary defenses. Shockwave, however, is not on board and retreats into cybertrons underground.
Sentinel furiously attempts to order the autobot forces but his use of a dangerous weapon out of pure aggression, within the sacred council chamber and endangering innocents has finally caused the autobots to turn on him.
Within kaon, megatron is being repaired and the cons have a moment of silence for lugnut then proceed to get acquainted/reacquainted. In the wake of lugnut's death, Megatron and starscream share some words of respect/insult towards each other and starscream takes his place as second-in-command again but is clearly already planning treachery.
On cybertron, sentinel has been stripped of the rank of magnus but, on optimus' advice and due to his service record, is allowed to remain a member of the council, which sentinel secretly hates and sees as optimus pitying him. To everyone's surprise, optimus has lugnut honorably memorialized, stating that he was just a bot who fell under megatron's spell. The council make optimus the supreme commander and name him Optimus Magnus and give him the hummer. Optimus declares that ultra magnus will keep his title and his weapon and hands the matrix over to the council to guard, especially from sentinal.
The autobots discover that kaons flight path shows that it is heading back towards earth, which optimus anticipated. Optimus intends to follow them on omega supreme and so leaves the autobot council in charge of cybertron while he is gone. Due to bulkhead being the greatest spacebridge expert on cybertron, optimus request that he stay on cybertron and makes him a member of the council. He then sets out after the cons in omega supreme with ratchet, bumblebee, jazz, arcee and new comer ironhide.
Hidden in a lower level of cybertron, shockwave arrives at the secret objective to him by megatron, a secret decepticon base. Inside is the small militia, including reflector, team chaar and others. The decepticons will subtly and over time cause trouble and panic on the planet so it will be in chaos when megatron eventually returns to conquer it.