On Cybertron, Alpha Trion prepares for his eventual capture by Shockwave. Although Ultra Magnus and the Wreckers are doing everything they can to impede and harass the Decepticons occupying the planet's major cities, Shockwave's forces maintain control of the planet's major cities, and the mad scientist has turned the occupied city of Iacon into his personal laboratory, viewing the Autobot resistance as mere tools used to cull the weak and enhance the strong. His new reign is symbolized by his new personal tower, wherein he conducts his brutal experiments. As Shockwave's guards and many Insecticons burst through his door to arrest him, Alpha Trion quietly gives himself up. Some time after the battle on Junkion, Starscream and Soundwave detect the energy signature of the Ark among an asteroid field. Megatron orders the Seekers to attack, but Starscream and his strike force discovers that the signal is a ruse engineered by Thundertron and the Star Seekers, who plan to wipe out the Nemesis with the Requiem Blaster. Taking advantage of the Blaster's high energy consumption rate, Megatron manages to best the pirate leader in hand-to-hand combat while the Nemesis overwhelms the Tidal Wave, forcing the pirates into a retreat. In the midst of the battle, Wreck-Gar manages to steal an escape pod and escape his captors, while Axer, once again converted to Megatron's side and hoping to regain his leader's favour, reveals to the Decepticon leader that he knows the true whereabouts of the Autobots… Elsewhere in space, Optimus Prime and the other Autobots aboard the Ark discover an aquatic, inhabited world rich with Energon that does not appear on any of the Ark's star charts. Optimus initially has reservations—the Matrix of Leadership has recently been transmitting strange and unsettling visions of subjugated Cybertronians, causing him to doubt his leadership—but he reluctantly orders a scouting party composed of Bumblebee, Rodimus, and Kup to land near one of the planet's cities. Back on Cybertron, Shockwave gloats to a captive Alpha Trion about his discovery of Vector Sigma, located deep below Iacon in Shockwave's newest tower. The Autobot away party are greeted on the surface by an amphibious being identified as "the Curator", who welcomes them to the peaceful, Energon-processing planet of Aquatron, rich with processed energon cubes and free of poverty, tyranny, or greed. Aboard the Ark, a worried Optimus consults with Ratchet about his recent visions, but the Autobot medic cannot find any physical problems. Beneath Iacon, Shockwave reveals his newest plan to his captive audience; having studied scraps of the Covenant of Primus, he plans to use Alpha Trion—the last remaining Prime on Cybertron—to unlock the supercomputer's true potential and forge a Decepticon Matrix of Leadership that will further enhance his control over Cybertron. Although Alpha Trion protests, knowing what Shockwave will unleash by doing so, Shockwave nonetheless orders him integrated into Vector Sigma's circuitry regardless. On Aquatron, Optimus makes planetfall aboard one of the Ark's shuttles, accompanied by his closest associates. Although Perceptor and Ratchet are impressed with the Aquatronian's vast supplies of Energon, Optimus suffers another vision of Orion Pax, his former self, threatened by a shadowy figure intent on enslaving him. The shock causes him to collapse, and the Curator suggests taking him to the nearest Aquatronian medical center to ascertain the problem. A sceptical Kup, Rodimus, and Bumblebee commandeer the Autobot scout shuttle and drive it underwater, in the hopes of discovering the truth behind the seemingly benevolent Aquatronians. At the medical center, the Autobots encounter Doctor Xeros, Aquatron's senior physician. While scanning Optimus, the doctor discovers his Matrix, which he immediately recognizes. Although Optimus eventually comes to and recovers from his shock, Jazz grows increasingly suspicious of Xeros and the Curator. In his private sanctum, the Curator examines the scans of Optimus's Matrix. After reporting to his supervisors, he reveals a replica Matrix that he begins tampering with, in the hopes of further destabilizing the already disoriented Autobot leader… Underwater, the three Autobots soon find themselves over their heads—literally, as their makeshift submarine crashes in a deep-sea trench, leaving them stranded beneath the sea. That evening, at an Aquatronian welcome ceremony, Ratchet confides in Optimus that his worrying visions may be tied to repressed memories of a traumatic experience, but before he can elaborate, Ironhide contacts him with news of the shuttle's disappearance. Optimus immediately orders a search and rescue mission to recover the trio, and the Curator pledges the support of all Aquatronians in the effort. Underwater, Kup, Rodimus, and Bumblebee eventually find themselves in a large underground complex filled with thousands of dormant Sharkticons. Before they can explore any further or contact, they are hypnotized by a series of glowing lights and abducted by the Curator, who restrains them and begins tampering with their minds. Meanwhile, on the outskirts of Iacon, Springer and Wheeljack rendezvous with Jetfire and Ultra Magnus. Having learned of Alpha Trion's predicament through inside contacts, the Wrecker leader has gathered them for a rescue mission. He introduces them to two additional recruits to the Wreckers: a deformed victim of Shockwave's experiments named Rack n' Ruin and a newly rebuilt Omega Supreme. In space, the Nemesis finally catches up with the Ark, and Megatron orders his troops to attack. Although the Aerialbots join the fray by combining into Superion and inflicting heavy damage on the Nemesis, they are cut short by the Curator, who cuts the power of both ships and scolds them for fighting in neutral space. With no other course of action, Megatron is forced to accept the Curator's invitation to declare a temporary truce with the Autobots and descends to the planet below. With the Autobots and Decepticons now stranded on the planet, the Curator reveals the truth—he is in reality a Quintesson, and Aquatron is now a part of the Quintesson Co-Prosperity Sphere, ostensibly a peaceful federation of trading partners. Optimus, who remembers reading about the hostile Quintesson occupation of Cybertron during his days as a data clerk, has his doubts about the Curator's true intentions, as do Ironhide and many of the other Autobots. The Curator requests that both factions maintain their truce for at least twenty-four hours while Optimus and Megatron attempt to negotiate a peace treaty to permanently end their civil war. Ultra Magnus and his crew manage to sneak through Iacon's fortified borders and into the city's interior. Magnus directs them to his contact, who turns out to be Maccadam, the proprietor of Maccadam's Old Oil House, who has turned his bar into the hub of the Autobot resistance's spy network. That night in the Pavilion, Optimus, Starscream, and Megatron are all visited by the Curator, who promises something different to each one: knowledge of the AllSpark's location, command of the Decepticon cause, and a Decepticon Matrix of Leadership, respectively, should they cooperate the next morning. Starscream, however, has other plans. On Cybertron, Shockwave has trouble using Alpha Trion to unlock Vector Sigma, as the old archivist has taken the precaution of inserting a failsafe code around his own cortex. Trion tries to reason with the scientist one last time, warning him that tampering with Vector Sigma could have dire repercussions for the entirety of Cybertron, and could very well draw the attention of unsavory forces. Shockwave ignores him and begins pumping Dark Energon into Vector Sigma, to Alpha Trion's horror; the Prime knows that Shockwave's experiments have awakened something terrible and alerted them to the presence of Cybertron. Meanwhile, the Curator and Xeros, sensing the reactivation of a long-dormant Space Bridge on Cybertron through Vector Sigma, reactivates the cryogenically preserved General Tyrannicon, and prepare for an impending invasion… The following morning, Starscream recruits Skywarp, stroking his ego by lying about a personal mission from Megatron. Skywarp uses his teleportation powers to plant a bomb beneath the Pavilion in the hopes of killing both Optimus and Megatron, allowing Starscream to defeat the Autobots and seize control of the Decepticon forces. When Optimus meets Megatron for the peace conference, the Decepticon leader reveals his true intentions as he deploys a hidden squadron of Vehicons, believing that he will be rewarded for his efforts. Before the two can complete their fight, however, the bomb explodes. Skywarp is grievously wounded and crashes into the sea below, while the assembled Autobots and Decepticons in the Pavilion blame one another and begin fighting. Optimus and Megatron mange to make a narrow escape from the flooding chamber. To quell the increasingly upsetting visions of the Quintesson-manipulated Matrix, he is forced to switch it off, but in the process he cuts himself off from the Matrix's supplies of wisdom and energy. The two manage to escape back to the surface and rejoin their troops, but promptly encounter a massive armada of Sharkticons and their general Tyrannicon, who places both Autobots and Decepticons under a humiliating arrest. Maccadam's network of informants allows the Wreckers to pinpoint Trion's location, but Senator Ratbat has managed to track them back to their base. To deal with the Decepticon police forces, Ultra Magnus orders Omega Supreme to bombard the city, clearing a path for the team to make good their escape. When the Cybertronians arrive via prison transport to the Aquatronian's capital city of Hydratron, Optimus is immediately sent to stand trial for his numerous “crimes” against the Quintesson Imperium. The Quintesson high court holds Optimus, and, by extension the rest of the assembled Cybertronians, guilty of treason against the Quintessons and blasphemy against their creators. The Quintesson prosecutor claims that his race travelled to Cybertron long ago and built the first Transformers, benevolently guiding their developing civilization until they were driven off-planet by their rebellious creations. Optimus is initially swayed by this story before he finally recalls his suppressed memories, including a life before the duplicitous Quintesson invasion, and denounces the Quintessons as liars. To his horror, his own soldiers – the brainwashed Kup, Rodimus, and Bumblebee—testify against him anyway, claiming him to be a warmonger and a relentless murderer. Their testimony is backed up by the scavenged remains of Skywarp, who also testifies against Prime and accuses him of planting the bomb. Of all the people in the court, Megatron himself supports Optimus's claims, arguing that the data clerk did nothing in the war that ousted the invaders. The Quintesson judges, after some consideration, find Optimus Prime and the rest of the assembled Cybertronians innocent… and start to execute them all, by pushing them one by one into a Pirahanacon-infested pool. The Quintesson judges tell the two leaders to fight one another in hand-to-hand combat; whoever wins will be able to leave the planet unharmed after killing the loser. With no other option, the two comply. Unbeknownst to them, the Curator is secretly harvesting the energon emitted in the fight to charge up a space bridge hidden beneath Hydratron. Shockwave's experimentation with Vector Sigma have pinpointed the current location of Cybertron, and the Quintessons have assembled the Sharkticon army to invade and re-colonize the Transformer homeworld. Before Optimus and Megatron can conclude their duel, the floor abruptly opens up beneath them and sends them tumbling into the Pirahanacon pit—the space bridge has activated, and they are no longer needed. On their respective ships, Starscream and Sideswipe pick up abnormal energy readings and independently come to the conclusion that their leaders are still alive. The Autobots and Decepticon flagships prepare to assault Aquatron and recover their leaders. Beneath Iacon, Shockwave's experiments are interrupted by the timely charge of the Wreckers, who steamroll Shockwave's Insecticon guards and detach Alpha Trion from the interface, even though the mad scientist himself slips away in the mayhem. Alpha Trion, cognizant of the coming danger, tells his rescuers that their entire world will soon need saving from the coming invasion force. Optimus and Megatron manage to fight their way out of the execution chamber and into Aquatron's subterranean layers, although to do so Optimus must reactivate the Matrix, once again exposing himself to a stream of Quintesson propaganda. Simultaneously, the Ark and the Nemesis launch a joint attack on Aquatron's defence systems. In retaliation, the Sharkticons successfully shoot down the Nemesis, but the Ark manages to deploy an Autobot strike force headed by Sunstreaker to reinforce the surviving Transformers, who are pinned down by Sharkticon forces under Gnaw's command. Jazz and Starscream form a temporary alliance to defeat the Sharkticons. The rest of the Sharkticon armada, headed by Tyrannicon, reaches Cybertron and swiftly overwhelms the largely abandoned world, seizing both the Well of All Sparks and the Vector Sigma terminal as beachheads. The main invasion force continues to move toward Iacon. Optimus and Megatron, now lost underground, encounter a monstrous techno-organic beast calling itself the Gamekeeper, who taunts the duo about the current Quintesson invasion of Cybertron already in progress. Although they manage to defeat the Gamekeeper, Megatron discovers a mysterious set of carvings, depicting a warrior not unlike himself surrounded by Sharkticons. Megatron is intrigued, but Optimus is sceptical of their veracity, even after the dying Gamekeeper confesses that they were carved by an unsuccessful Sharkticon rebellion seeking to overthrow their Quintesson masters. Tyrannicon's forces reach Iacon and begin their main assault. Although challenged by Omega Supreme and Devastator, the Sharkticon general impales the Autobot guardian through the head and buries the combiner under a collapsed building, putting them both out of action. In Hydratron, the impromptu alliance between Autobot and Decepticon begins to fracture as the Transformers are swiftly pushed back by their enemy's weight of numbers. The combined force quickly evacuates the battlefield and takes shelter in the downed Nemesis. Gnaw retaliates by gradually submerging the city, intending to force the Cybertronians out of their shelter. Meanwhile, Megatron and Optimus temporarily elude their Sharkticon pursuers by breaking into the Quintesson's inner sanctum, where they discover Xeros. An enraged Megatron interrogates him and demands to know the Curator's location, but Xeros refuses to divulge the information. In frustration, Megatron pounds a nearby console, revealing, to his elation, the decoy Matrix the Quintessons used to manipulate Optimus's memories and emotions; a device Xeros also used to control the Sharkticon forces. Believing it to be his promised Decepticon Matrix, Megatron plunges it into his chest without a second thought. As the Sharkticons close in on Iacon, the Wreckers head for the Hall of Records and the archives therein. Alpha Trion plans to detonate the entire building to prevent valuable information from falling into the hands of Tyrannicon's forces; meanwhile, Shockwave desperately seeks out the various he could use to repel the invaders, only to find that none of them remain in his formerly secure vault—Alpha Trion has already ejected them from Cybertron. Furious and fearful for the future of Cybertron, he enters the archives and demands that Alpha Trion stop his scorched earth plan, only to be interrupted by Tyrannicon and his new aide, Senator Ratbat, who has allied with the Quintessons in exchange for being made the governor of Cybertron. In desperation, Alpha Trion pushes the detonator… only for nothing to happen—Tyrannicon preemptively jammed the detonator's frequencies. Underneath Aquatron, Megatron's new Matrix imparts new knowledge to his mind as it changes his body. Aquatron really is one of the lost Cybertronian colony worlds, one that was invaded and subjugated by Quintessons in the distant past. By tampering with Matrix technology, the Quintessons in reality, created a Sharkticon Matrix of Leadership, foreseen by the rebellion in the distant past as the artefact that would one day lead the Aquatronians to freedom. With Megatron's body reshaped into an avatar of the Sharkticons, he casually orders his new Sharkticon troops to attack Xeros while he throws Optimus down an elevator shaft. All across Aquatron and Cybertron, the Sharkticons revolt on the command of their new god, bringing the invasion to a grinding halt, while Megatron orders every Sharkticon on the planet to find the Curator and kill him. As Optimus plunges to certain doom, he is visited by a mysterious apparition of thirteen silhouettes, who tell him that his time has not yet come and that he is exactly where he needs to be. The Autobot leader plunges into the jaws of a Leviacon, a gigantic peaceful mechanoid recently freed frm the yoke of Quintesson control. Optimus orders the Leviacon to head toward the lake bed so that he can confront the Curator and destroy the space bridge. Just when it seems Tyrannicon is about to seize control of the Hall of Records and finish off the Wreckers, his Sharkticon troops rebel against their leader, allowing the Wreckers to escape and regroup. With his invasion of Cybertron usurped, Tyrannicon heads back toward the space bridge in the hopes of confronting the one responsible. Rack n' Ruin takes advantage of the confusion to split off from the rest of the group, steal the detonators, and cheerfully rig Shockwave's tower to explode. Shockwave, however, has already departed from Iacon, but vows to find a new way to make every Autobot suffer for the destruction of his laboratory… Megatron's rebel Sharkticons soon swarm toward the space bridge, where they run up against the Curator's fortified command bubble. A frantic Curator tries to lie to his superiors that the invasion was a success, but they do not believe him. As the city continues to sink, the Ark arrives to evacuate the Autobot forces, much to Starscream's chagrin. The Autobots agree to help the Nemesis back into orbit. Starscream is contacted by Megatron, who has declared himself the new lord of Aquatron and begins loading his new Sharkticon troops aboard the Nemesis as proof of his new powers. As Megatron makes for the Nemesis, he is taunted by the Curator, who reveals to him that the entire city is a living, bioengineered being –the Hydratron, who will travel through the space bridge and consume every Cybertronian in existence. Megatron and his new Sharkticon retinue fight their way through the beast's innards before arriving at the Space Bridge. The transformed city attacks the Ark/Nemesis combo, and even though Superion tries to repel its attacks the Hydratron proves too strong to overpower, and begins dragging both ships into its gigantic maw. While Megatron breaks free of the Hydratron's stomach and heads toward the Curator's lakebed space bridge, Superion arrives just in time and manages to boost both ships out of the Hydratron's reach, carrying the Autobots and Decepticons to safety. Optimus and the Leviacon arrive just in time to confront the Curator. The Curator taunts Optimus, claiming that he'd been playing the Autobot leader for a fool all of this time before he knocks him unconscious with a wand-like device. Suddenly, Tyrannicon bursts through the Space Bridge, intent on ending the Curator's machinations once and for all. The general easily tears the Curator's outer shell in half, revealing a tiny organic squid-like creature who begs for mercy, shortly before Tyrannicon crushes him. Megatron finally arrives, now bent on subjugating Aquatron. He offers Tyrannicon a position as his new general. Tyrannicon, outraged, easily bests Megatron in combat before stealing the Sharkticon Matrix, further enhancing his capabilities and once again granting him control over the Sharkticons. Before he can kill the Decepticon leader, however, the descending Hydratron grabs him and eats him. As Optimus barely regains consciousness, he realizes what he has to do. Using the Curator's wand, he manages to ignite the energon fuelling the bridge, causing a cataclysmic chain reaction that destroys the ancient Space Bridge entirely. Aboard the two ships, morale runs low as Autobots and Decepticons scan the seas for a sign of their leaders. Just as they are about to give up hope, Sideswipe sees the Leviacon surfacing, with a weary but triumphant Optimus on his back—and accompanied by Megatron. With the Matrix once again purified and free of Quintesson control, the Ark takes off into deep space as Optimus Prime and the Autobots resume their search for the AllSpark. Meanwhile, on Cybertron, Alpha Trion resumes studying the Covenant as he muses about the future. In particular, he wonders about the Iaconian relics that he sent to a peculiar planet on the fringes of the Orion Arm—a small, blue-green world...
- Optimus Prime
- Hot Shot
- Omega Supreme
- Shockwave has rebuilt his tower for the second time; his first tower in the Sea of Rust was destroyed by Jazz and Cliffjumper, while Grimlock destroyed his second tower in Kaon during the events of Fall of Cybertron. Shockwave should just really stop trying to build towers at this point.
- Shockwave mentions to Alpha Trion that he is aware of the fact that Optimus is in possession of the Key to Vector Sigma, which was previously mentioned in "One Shall Rise, Part 3".
- Ultra Magnus has completed repairing Omega Supreme, who was previously badly wounded in War for Cybertron and required extensive repairs, even after he was purged of Dark Energon.
- Many of the relics that Shockwave seeks are artifacts from the Prime cartoon, including the Star Saber and Tox-En.
- Alpha Trion reveals to Shockwave that he had already ejected all of these same artifacts to Earth, which was previously established in "Alpha/Omega".
- On page 19 a Seeker named Debris says he's picking up energy readings. This is clearly a typo for Dirge as Starscream, Thundercracker, Skywarp, Thrust, Dirge, and Ramjet are the only ones sent out.
- On page 64 Shockwave frowned.
- On page 206, Sunstreaker states that Bluestreak, Trailbreaker, Mirage, and he could retrieve Optimus Prime using a combat shuttle, but "Chapter 7: The Golden Age" in The Covenant of Primus shows that Bluestreak was left on Archon when the space bridges were shut down due to the Rust Plague.
- The Quintessons' plan is a bit of a head-scratcher. The Curator powers the Space Bridge to Cybertron by killing the Cybertronians off one-by-one and harvesting their energon as a power source. But Aquatron supposedly has warehouses full of energon, seemingly far more than the crews of the Ark and Nemesis have inside their sparks, so why not just use that?
- The Curator ultimately powers the Bridge with the unique and powerful energies of the Matrix, which the Aquatronian energon may not have been able to produce, but this is clearly Plan B -- only after it was reported that the standard executions would not meet the energy quota did he alter his plans to make Optimus turn the Matrix back on.
- On page 290, Ratchet is stated to be among the Wrecker's rescue crew.
- On page 327 Skywarp is flying beside the Ark when he was devoured by Gnaw.
- On page 328 Ramjet is helping Megatron when he was one of the first ripped apart by the Piranhacons.
- On page 328 Slipstream is also helping Megatron when she was previously abandoned over Junkion in Exiles.
- In Exiles, Silverbolt was said to be the only Autobot aboard the ship capable of independent flight. Here, all five of the Aerialbots appear as members of the Ark, with no explanation for the discrepancy.
- As the first installment in the Aligned continuity family to properly feature the Quintessons, multiple references to their previous incarnations—in particular, their iconic Generation 1 appearances—abound.
- The Quintessons claim that they settled Cybertron in the distant past and built the first Cybertronians, recalling the events of "Five Faces of Darkness, Part 4", which also featured Quintessons overseeing the creation of the Transformers and a subsequent rebellion that drove the Quintessons off the planet.
- Optimus Prime suffers visions of Quintessons overseeing assembly lines of Cybertronians, a scene lifted almost directly from the same episode.
- As per their first appearances in the 1986 animated film, the Quintessons' fondness of kangaroo courts forms a major scene in the novel, as does their proclamations of "innocence" that are apparently synonymous with being guilty.
- The Quintesson sentence for "innocent" involves being pushed into a watery pit full of ravenous creatures and devoured, a fate first encountered by Kranix in The Transformers: The Movie
- The Curator originally describes Aquatron as a world affiliated with the Quintesson Co-Prosperity Sphere, a term first used in the Allspark Almanac II.
- Kup and Rodimus are among the first members of the scouting party to encounter the Quintessons, as their Generation 1 counterparts did in the movie.
- Kup chews on cy-gars in a nod to his IDW counterpart.
- Rodimus's weapon of choice is the same as his Animated counterpart.
- When Megatron places the Matrix replica into his chest, his new body is clearly based off the Beast Hunters Voyager Sharkticon Megatron figure.
- Wreck-Gar uses several British slang terms such as "guv'nor" in his dialogue, likely as a reference to his original voice actor Eric Idle.
- Megatron's cry of "GET OFF MY SHIP!" to Superion may be a reference to the famous line spoken in the 1997 film Air Force One.