Pillar of Wrath:
Stories in this arc tend to follow Jude, and focus on the past. Specifically, how Jude transformed from being an altruistic college student, to a hardened soldier, directly due to his involvement with killing the rogue manipulator, Nicolai.
Pillar of Wisdom:
Stories in this arc tend to follow Feynman, Dr. Bryant and Barrette as they attempt to exfiltrate Fatima out of the country, and is set in the modern times. The key goal of this arc is to establish the motives of the Synaxis.
Pillar of Mercy:
Stories in this arc tend to follow Maria Salazar and Jupiter Black, and focuses more on the history of the Pantheon Project, specifically how manipulators are created, and what happened to project as a whole. The stories are set across the lifetime of the project, and therefore can appear in the past and in modern times. Dirac makes numerous appearances in this arc as well because of this.
1: Malkhut - KINGDOM
Introduce characters, kill Dirac.
2: Yesod - FOUNDATION (Wisdom)
Save Barrette, introduce Jude and the resistance. Explain Feynman's condition, specifically him missing his son's wedding, and appearing at the church several years after due to his condition, mistakenly believing it to be the correct time.
3: Hod - GLORY (Wrath)
The first Wrath story. Switches between the present day, with Barrette and Jude describing the existence and extent of the PANTHEON project, and the past, wherein Jude relates his "education" as a manipulator. Barrette, Feynman, and Dr. Bryan search for clues about the whereabouts of Maria, Fatima, and Jupiter Black.
4: Netzach - VICTORY (Mercy)
Maria's first story. In the present, Barrette and Dr. Bryan have located Maria, and believe her to be present within an upstate mental hospital, which is in reality, a holding center for retired manipulators. Maria relates her border crossing, and deployment to columbia in the 90's.
5: Tiferet - ADORNMENT (Wisdom)
Feynman and Barrette locate the Glockner server cache which holds the names of all first and second wave manipulators. An assault is planned and conducted. Feynman is able to use his powers of magnetism to destroy the electronics of the facility, causing the Synaxis to lose all data on every manipulator up until this point, essentially setting them free. Jupiter Black intercepts them during the assault, and liquefies Feynman with his powers over radiation.
6: Gevurah - JUDGEMENT (Wrath)
Returning to Jude's original narrative, we see Jude now in 90's Chechnya, having been assigned the mission to find, and possibly recruit, a suspected manipulator. While Jude makes his connections throughout the besieged locales, he makes contact with a priest who runs an orphanage: Nicolai. After spending sometime with the orphanage, a stray bomb endangers the children. Jude reacts out of instinct, and uses his powers over gravity to save those that he can, revealing himself to Nicolai as a manipulator. Nicolai then approaches Jude with this information, and asks that he side with them in the conflict. When Jude declines, and asks that Nicolai instead return to the United States with him, a battle ensues. Jude, in his inexperience, is defeated. Jude makes a request to his handler to allow him to "educate" a possible candidate in the field, so that he can bring back up to his rematch against Nicolai: the son of General Graves, Weston Graves, who will later become Jupiter Black.
7: Hesed - KINDNESS (Mercy)
Return to Barrette, Fatima, and Bryant, who are now using the list originally exfiltrated from the server cache to make contact with a list of Manipulators who were under surveillance by the corporation. They spend the next several issues/episodes doing just this at the behest of Jude, who's secret intent, unknown to even him, is to rebuild his contrarian sephirot group in preparation for the maneuvers of the Synaxis.
8: Binah - UNDERSTANDING (Wrath)
Alternating between the present, and Jude's mission to Chechnya, we see that Weston Graves has not taken so well to the manipulator education, and with the limited resources available to them in the blasted out remains of Chechnya, he will likely die. Jude again confronts Nicolai, who has at this point raised a child army of prodigal manipulators. A battle again ensues between the two of them, with Jude finally emerging as the victor after destroying a large amount of nearby military equipment (and/or personnel). Nicolai notes the regret that Jude has in taking his first life, and contemplates how in a way he has killed a part of himself. This is a nod to the fact that all manipulators harbor a vestige of the EDI in the material world.
9: Hokmah - WISDOM (Mercy)
Maria drowns her children. Jupiter Black murders his father. Fatima is recovered.
10: Keter - CROWN (Ending)
It is the apocalypse. The Synaxis attempt to pull through a "host vehicle" for the next stage of human physical and spiritual evolution via a ritual sacrifice (i.e. the extinction of mankind in a bridging event). It is revealed that the AKASHIC Super Computer was only half of the original 10 Berkeley notebooks; the other five were dedicated towards the construction of a theoretical particle accelerator, which could sustain a bridging event large enough, and long enough, to offer up the whole of humanity. AKASHIC was only intended to process the data to allow for the construction and use of the larger device.
Meanwhile, Jude, who has come to accept his loss of identity to [Apollyon?*], seeks to return to the greater realm from whence his possessing entity emerged.
10.5 Da'at - REFLECTION