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Siege and Nightstar have discovered information that agents of Primal Earth are planning to infiltrate the Behavioral Adjustment Facility, better known as BAF. They make a report to Mother Mayhem in which they will spin the infiltration as an unprovoked attack, and in the meantime, release brainwashed members of the Resistance who will relay messages about the beneficence of the Praetorians. At the same time, the infiltrators will be forced to let the confused Resistance leave and foil their plans to collect information, or attack them for further bad press.
A group of Incarnates allied with Primal Earth seek to deprive Praetorian forces from access to one of their primary weapon storage facilities to help dismantle the war that has broken out between the two dimensions. However, Marauder is on staff to stop them in their tracks. The Incarnates destroy a number of the weapons stored in the Lambda Facility and face off against Marauder after he quaffs a formula to boost his powers designed by the Praetor of Science, (a.k.a. Anti-Matter), as they attempt to make their escape. Marauder is taken into custody after the battle and Praetoria is left with fewer weapons of war.
The reactor housed on Keyes Island built by Anti-Matter supplies the majority of power to Praetoria. A team of Incarnates plan to disable it to cripple Praetoria's war effort. Unfortunately, Praetor Keyes (Anti-Matter), has caught wind of this plan and set his Clockwork in motion to protect it. In addition, his suit has controls for the reactors and has set each of them to irradiate the whole island in turn if Primal Earth's allies don't work quickly to shut them down!
Keyes is ultimately defeated in a final showdown after all of the reactors have been successfully shut down.
The all but abandoned subway and access tunnels beneath Praetoria has been the home to the Resistance, working from below the city to slowly bring it down. Desdemona plans to meet a group of Incarnates and lead them through the tunnels into the belly of the beast to rescue Vanessa DeVore from the monsters that dwell there alongside the Resistance. However, the passage is not without its perils and is guarded heavily by the IDF lest anyone finds out one of Praetoria's darkest secrets.
After defeating an Extinction War Walker or two, and a score of the IDF, the allies find that Vanessa DeVore has already been slain, and that an Avatar of Hamidon killed her to keep her silent. However, Desdemona dons her fallen mask when the beast has been defeated and finds out that Emperor Cole made a deal with the Hamidon to keep it at bay, a deal that forced Praetoria's Marcus Cole to attempt the destruction of Primal Earth to keep his end of the bargain!
After finding out that Emperor Cole had made a deal with the Hamidon in the events that transpired in the Underground, a team of Incarnates are dispatched to the campus of the Total Praetorian Network to spread the word to all of Praetoria, since it is the only network on which Praetorians receive information.
Not surprisingly, the Emperor wants to prevent the news from getting out and having all of Praetoria turn against him, so he sends Maelstrom and a group of Seers to stop them. While Maelstrom attempts to stop their efforts directly, the Seers set about their work inciting Praetorians into an angry mob while simultaneously trying to warp the minds of the Primal Earth allies present so that they don't pose a threat.
In the end, Maelstrom is defeated, but the efforts of the Incarnates are in vain as the message is not broadcast across all of Praetoria.
In Mother Mayhem's private playground, the Mother of Mercy Psychiatric Hospital, a certain psychic is being held captive: Aurora Borealis. A group of Incarnates plan to free her. Their efforts are co-ordinated by Metronome, the Praetorian counterpart to the Clockwork King; Calvin Scott, the leader of the Resistance; and Desdemona who, having donned Vanessa DeVore's mask, is an important member of the Resistance as well.
Unfortunately, Malaise has been sent by Mother Mayhem to stop the team from ever reaching the inside of the Hospital. He summons a formidable collection of Nightmare illusions, but ultimately the team gets past him. Not to be so easily thwarted, Mother Mayhem possesses the bodies of several psychics within the hospital in order to stop the team: first Penelope Yin, then Aurora herself, then Malaise, and finally the team is thrust into Mother Mayhem's Seer Network itself to defeat her disembodied astral form.
In the end, the team frees Aurora and Penelope from Mother's control, and Calvin discovers that he was never married to Aurora at all, but that he was a former patient of the hospital.
Following the emergence of Mot from Moth Cemetery in Dark Astoria, a team of Incarnates is dispatched by the Dream Doctor to stop Diabolique from using Mot's vast otherworldly powers for her twisted purposes. The Incarnates must free a series of heroes from her control, face the Sentinel of Mot, and defeat Diabolique herself inside the body of Mot (along with two heroes she is controlling).
After the Incarnates take her down, the Dream Doctor, still possessing the Dagger of Jocas, kills Diabolique.
The Incarnates set up a bold plan to face down Tyrant, the Emperor of Praetoria. Their effort is co-ordinated by the Dream Doctor, and Dreamspace is used as a staging area. This allows the Dream Doctor to intervene should an Incarnate fall in battle.
In order to face off against the emperor, the Incarnates must face down against the remaining members of the Praetorian Guard: Black Swan, Nega-Pendragon (a negative of the Praetorian counterpart of Hero 1), Chimera (Praetor Sinclair) and Shadow Hunter (counterpart to Woodsman). Finally the team meets up with the emperor himself, but not before he institutes a "scorched earth" protocol and nukes the courtyard of the Magisterium killing potentially millions of Praetorians. Then, the emperor empowers himself with the souls of the dead (via the aspect of Hades that he absorbed instead of Praetorian Stefan Richter) and the final confrontation begins.
The Incarnates are able to vanquish the emperor who, having failed to keep his bargain with the Hamidon, sentences the rest of Praetoria to attacks by the beast and his minions.