Millennia after the events of Elohim Eternal: Exodus, Kenoma is once again divided into two people. The Pleromans live in a high-tech utopia in the northern part of the planet while the Shemerians live in the southern part of the planet. The Pleroman Empire conquered Shemer under the rationale that their people are in danger of transforming into feral monsters known as Archons. Shemerians live in impoverished towns that are heavily policed by Pleroman soldiers, who abuse their authority and frequently arrest Shemerians for being suspected of being on the verge of transforming. The protagonists are Judas, Jessua, and Lena, a trio of Shemerians who join the Zealots resistance group. Jessua has mysterious powers that cause many to believe he's the Monad's prophesized messiah, who will save the Kenomans from the Demiurge, and the Zealots hope this power will give them an edge against the Pleromans. Unfortunately, a mysterious instigator seeks to manipulate both sides of the conflict and throw Kenoma into chaos.
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This game contains examples of:
- All-Loving Hero: Jessua is a Decon-Recon Switch. He believes that as the messiah, he should save both Shemerians and Pleromans, despite the latter being the oppressor of the former. However, he has never met any Pleroman civilians, instead only ever meeting malevolent slavers and soldiers. As a result, he doesn't have a strong foundation for his beliefs and loses faith in Pleromans after being shown a vision of their atrocities. This causes him to take over the already radical Zealot resistance group and take them on a suicidal campaign against the Pleromans. As he's being executed, he sees how much he made both sides suffer with his actions, and he comes back as a ghost with his old ideals again.
- The Bad Guy Wins:
- After the party kills Caiaphas, who secretly sacrifices Shemerians to the Demiurge, the Demiurge unleashes their laser upon Kenoma once again, killing anyone who couldn't evacuate. The Demiurge then use this event as an example to cow the Idinites into submission.
- Nicodemus successfully tempts Jessua into becoming a mad warlord and ensures that peace between the Pleromans and Shemerians is impossible. He also rats out the location of the transmigrator to force a confrontation between the party and Caiaphas, and then kills a wounded Caiaphas, causing the Demiurge to destroy the surface of Kenoma after their proxy is killed. The only thing he fails to do is retrieve the spear containing samples of Jessua's blood, but aside from that, he still manages to bring about the chaos that his master, the Accuser, desires.
- The Battle Didn't Count: The fight against Pilates's Azar, Enkidu, ends with the battle being cut short and him being at an advantage in the following cutscene, no matter how well the player is doing.
- Be Careful What You Wish For: Judas despises the Pleromans for oppressing his people, the Shemerians, and seeks to join the Zealots rebel group in order to overthrow the government. He also hopes that his All-Loving Hero friend, Jessua, can use his messiah powers to defeat the Pleromans. However, he starts having second thoughts when Simon orders Pleroman civilians to be killed. Worse yet, Jessua becomes more radicalized and violent than the other Zealots and leads them down a bloodier path, which scares Judas.
- Jessua: You said so yourself that the messiah was a warrior king. You should be happy.
- Being Evil Sucks: The warden of one of the sanctuaries seems to be uncaring of his crimes against the Shemerians, but it turns out he knows about the Demiurge/Kosmokraters and fears their wrath if the Pleromans don't sacrifice Shemerians to them. Once the party fatally wounds him, Jessua realizes that the warden secretly regrets what he has done and hopes the Monad will forgive him.
- Break the Haughty: After Jessua goes mad from receiving the memories of persecuted Shemerians and becomes the leader of the Zealots, he starts becoming more prideful about his status as the messiah, to the point where he conflates his own personal vengeance with Shemerian liberation. In the endgame, the Pleromans wipe out his resistance, Nicodemus reveals Jessua was never the prophesized messiah, the Pleromans torture and execute him, causing him to realize that his arrogance became his downfall. After coming back as a ghost, he reverts to his previous All-Loving Hero self and holds off the Demiurges' laser to save as many people from both countries as possible.
- The Chosen One: Double subverted. Jessua displays miraculous powers like undoing archon transformations and healing the sick, making it seem like he's the messiah chosen by the Monad. Nicodemus reveals this is not his own power, but rather, an irregularity with his Somanites. Jessua later realizes that Hashem, an implied divine being, was the one who lent her power to him and altered his Somanites.
- Contrasting Sequel Antagonist:
- The Pleroman Empire is less upfront about their Fantastic Racism than the factions in previous games. In public broadcasts, they take a stance of Condescending Compassion and claim they need to occupy and arrest Shemerians for their own good, and that theoretically it's possible for Shemerians to move up the caste system if they master Gnosis. When not on camera, the government leader and soldiers openly dehumanize Shemerians. Additionally, the Pleroman citizens are more open to the idea of coexistence, which is why the government cannot publicize their atrocities against the Shemerians, unlike the Misru who never make a secret of their misdeeds due to their slave system being completely normalized.
- Nicodemus and his master, the Accuser of all humankind, serve as this to the Demiurge/Kosmokraters. The Demiurge almost always establishes oppressive and hierarchal, but stable societies, which they claim is for the greater good of humanity but really for their own power and authority. In contrast, the Accuser and Nicodemus want to spread chaos for its own sake and are more open about being wholly evil.
- Contrasting Sequel Main Character:
- Judas at first seems just as brash and vengeful as Joshwa, but turns out not to have same degree of rage issues or Black-and-White Insanity, since he becomes disturbed when Jessua and Lena become increasingly vengeful and vicious against the Pleromans, and is appalled when his fellow Zealots kill Pleroman civilians.
- Jessua is meant to contrast Moshe, the protagonist of Exodus. Although Moshe rebelled against the Misru Empire, he treated the plagues as a necessary evil and took no joy in unleashing them upon the citizens of the empire, partly because he was raised by the Misru. Jessua starts out wanting to save Shemerians from Pleromans and wants to seek peace with the latter, though he has only ever seen the malevolent Pleroman soldiers rather than the civilians and he loses his mother to the Pleroman slave system, meaning he has little foundation for humanizing Pleromans. When he receives visions of the Pleromans' atrocities, he abandons his ideals and seeks vengeance against the Pleromans, believing all of them to be evil. It's not until he's publicly executed that he realizes the Pleromans fear him for his extreme actions and that he ended up hurting the Shemerians, causing him to regain his desire to save both nations. Finally, both use their powers to mitigate the damage from the Demiurges' laser as much as possible, though Moshe sacrifices his life in the process while Jessua is already a ghost when he does this.
- Create Your Own Villain: Judas convinces his friends Jessua and Lena to join the Zealots with him. This backfires when it turns out the Zealots are more radical and willing to harm civilians then he expected. Jessua ends up becoming a vengeful warlord after receiving a vision of all the atrocities the Pleromans committed, causing Judas to regret that he unwittingly caused his friend's downfall.
- Cyberpunk: Millennia after the events of Exodus, Kenoma's technology has advanced far beyond modern Earth's, as shown by how Pleroma can manufacture mechs known as Azars. Compared to previous games, the tilesets are more technological and futuristic, even in the relatively poorer towns like Nazareth. However, the Pleromans get to use this technology to live prosperously while the Shemerians are forced to live in poverty, are brutalized by Pleroman soldiers patrolling their towns, and have comparatively limited access to technology, though the Zealots resistance group managed to steal an airship and some Azars from the Pleromans.
- Death Equals Redemption: Jessua becomes a Fallen Hero in the endgame and leads the Zealots in a suicidal campaign against the Pleromans for the sake of revenge. After he's crucified, he comes back as a ghost to save as many people as possible from the Demiurges' laser, having seen the error of his ways.
- Deconstructed Character Archetype: Jessua is meant to deconstruct the Messianic Archetype, or according to the developer, the warrior king archetype that many of Jesus's peers expected him to be. Jessua ends up becoming a ruthless warlord who wants to wipe out the Pleromans and start a suicidal battle against them, believing that doing so is the only way to save his people. Additionally, his Sanity Slippage is due to him suddenly receiving the memories of Pleroma's victims, which is akin to him attempting and failing to bear the sins of humanity. In the endgame, it turns out Jessua is a regular mortal who was given a portion of Hashem's power.
- Despair Event Horizon: In Osiris's fossilized body, the party finds Haron, one of the protagonists of Exodus. He has given up all hope in rebelling against the Demiurge/Kosmokraters because of their Leviathan and Behemoth laser and because the Somanites can rewrite memories, which he sees as an insurmountable advantage. Instead of continuing the fight against the false gods, he just wants to live out the rest of his days in solitude.
- Dragon with an Agenda:
- High Baptist Caiaphas acts behind Emperor Tiberius's back by trafficking Shemerians to the Demiurge/Kosmokraters through the Transmigrator.
- Nicodemus is a Pleroman official who is supposedly subservient to Pontius Pilate and Emperor Tiberius. He is actually an agent of the Accuser of all humankind, who seeks to bring chaos to Kenoma.
- John is a high-ranking baptist in the emperor's inner circle, who secretly helps the Zealots resistance group.
- Everyone Has Standards:
- Judas hates the Pleromans for oppressing the Shemerians and joins the Zealots to rebel against them. However, he is against killing civilians and is appalled when his comrades do so in vengeance.
- Although Simon is willing to kill Pleroman civilians and intially goes along with Jessua's more radical leadership of the Zealots, he has second thoughts when he realizes Jessua cares more about revenge than the actual feasibility of his attacks on Pleroma.
- Fantastic Caste System: From highest to lowest ranking, Kenomans are divided into Pneumatics, Psychics, Hylics, and Sarkics based on their proficiency with Gnosis. Sarkics are considered in danger of mutating into Archons, and are regularly rounded up and placed into facilities to contain them. In reality, all classes are equally vulnerable to transforming into archons, and the true criteria is stress, due to the somanites in the body mutating them. The caste system is made up for the sake of oppressing Shemerians, who have the least opportunity to master Gnosis due to enforced poverty by the Pleroman government.
- Fantastic Racism: The Pleroman Empire discriminates against the Shemerians, placing them at the bottom of the Gnosis-based caste, enslaving them, and sending them to facilities for experimentation. The government claims this is because Shemerians can transform into dangerous Archons, but in reality, all Kenomans can transform into Archons, regardless of race. The majority of the government wants to force Shemerians to transform into Archons to use as disposable tools of war against the Demiurge, while Skylar's Cult wants to sacrifice Shemerian prisoners to appease the Demiurge.
- Faux Affably Evil: Nicodemus Kastor seems to be one of the more polite Pleromans and is a better boss to work under than General Herod, but he's a Mad Scientist who performs experiments that frighten even other Kenoman scientists, and he has no empathy for anyone who suffers under experimentation. He outright states that he doesn't truly serve the Pleromans and that he wants to sow chaos and discord among humanity.
- From Nobody to Nightmare: In his introductory cutscene, Nicodemus claims he was once a slave who was beaten and shackled. Due to his immortality, it's implied that he was once a Simru slave during the days of the Misru Empire before joining the Accuser of all humankind.
- Giant Space Flea from Nowhere: The Final Boss is the spirit of suffering, an archon-like being who is the amalgamation of all the pain that the Kenomans went through, but its existence is only vaguely hinted at earlier through Pontius Pilate's nightmare.
- Go Mad from the Revelation: During Chapter 8, Lazarus dies protecting Jessua. Jessua then receives a vision of the Pleromans' atrocities, including General Herod raping Lena. This causes Jessua to become utterly ruthless towards the Pleromans, seeking to take revenge on them all.
- Happy Ending Override: While "happy" is a huge stretch, the Downer Ending of The Babel Code at least had the Idinites recover from their civil war and learn their Kosmokraters were manipulating them. In the ending of this game, the Kingdom of Rhea is subservient to the Kosmokraters.
- Hates Their Parent: Judas resents his father, Joseph, for being subservient to the Pleromans, who are oppressing the Shemerians. He later learns that Joseph used to be the leader of the Zealots, but lost his fighting spirit after the Time of Tribulation, where the Pleromans massacred many Shemerians, including his wife. Due to Judas's increasing doubts with the Zealots, he becomes more sympathetic towards his father.
- Heel–Face Revolving Door: Jessua starts as an All-Loving Hero who wants to bring peace between the Shemerians and Pleromans, but becomes genocidally vengeful against the Pleromans when he receives the memories of their victims. After his execution, Jessua comes back as a ghost and realizes that he should have stuck to his original goal of saving both races.
- Heroic Lineage: Downplayed. Judas turns out to be the great-grandson of Beyoz and Ruthia, the secondary protagonists of The Babel Code. However, Beyoz and Ruthia are only famous heroes on the planet of Idin, and not Kenoma.
- How the Mighty Have Fallen: The Zealots resistance group used to have far more members and resources, but Nicodemus Castor, a Pleroman official, somehow predicted their actions and hideouts. The Pleromans used this knowledge to enact the Time of Tribulation, a massacre of Shemer, in order to purge and capture all resistance members. In the present, there are only two active members, with everyone else quitting, getting killed, or getting captured.
- Hypocrite: The Pleromans claim to oppose the Demiurge's tyranny in the name of their first empress, Zipporah. However, they enact a caste system to oppress the Shemerians, and secretly sends Shemerians to slave camps under the pretense of preventing them from transforming into Archons. In practice, they are just like the Misru Empire that Zipporah overthrew.
- I Lied:
- Judas and Joseph sell out the location of the Zealots' HQ in exchange for the Pleroman sub-leader, Pontius Pilate, non-lethally capturing the rebels and sparing Shemer. Pilate immediately reneges on his promise by killing all the rebels, slaughtering much of Nazareth's population, and publicly executing Jessua. He states that he sees Shemerians as subhumans who aren't worth keeping promises to.
- Nicodemus threatens to turn Simon into an Archon if Jesse doesn't surrender to the Pleromans. When Jesse submits, Nicodemus gloats that he never keeps his promises and turns Simon into an Archon anyways.
- I've Come Too Far: In the endgame, Simon acknowledges that Jessua is becoming too extreme and reckless of a leader and that the next battle will be suicidal, but believes the Zealots have no choice but to continue following the latter, since at this point, they have killed far too many Pleromans to feasibly make peace. He turns out to be correct when Judas sells out the Zealots in exchange for mercy for the Shemerians, only for Pontius Pilate to renege on his promise.
- Jerkass Realization:
- James originally blamed Lazarus for the Pleromans foiling the first attempt at rebellion, since the latter is a Pleroman and the son of High Baptist Caiaphas. After Lazarus risks his life to bust the Zealot members out of prison, James apologizes and states he was wrong to distrust his comrade.
- Jessua suffers from Sanity Slippage and becomes more aggressive in leading the Zealots against the Pleromans. After his actions provoke a second genocide against the Shemerians and he gets crucified, he realizes he was wrong to use his powers for revenge and that he let his messiah powers go to his head.
- Jerk with a Heart of Jerk: Pontius Pilate, the second-in-command of Pleroma, appears to be one of the more reasonable members of the ruling class, as stated by Joseph, the governor of Nazareth. Although he's condescending towards the Zealots when he defeats them in Azar combat, he seems gracious enough to let them flee. He claims to be regretful of the Time of Tribulation and is seemingly willing to accept a non-lethal surrender of the Zealots if Judas sells them out. However, he breaks his promise and has most of the Zealots killed, wipes out much of Nazareth's population, and crucifies Jessua to Make an Example of Them, making it clear any prior mercy he showed towards Joseph was a ploy to keep him obedient. In reality, he dehumanizes the Shemerians just as much as the rest of the Pleroman ruling class.
- Mad Scientist: The Pleroman scientists experiment on Shemerians to turn them into Archons, with the intent of using them as shock troops against the Demiurge. Nicodemus is even more mad, since he comes up with new, torturous ways to turn people into Archons while circumventing any immunity or cure.
- Magocracy: The Pleroman castes are based on one's mastery of Gnosis. In theory, anyone can work hard to move upwards through the castes, but in practice, those who are already at the higher castes have more access to education, making upward mobility an extreme rarity in practice. As a result, few if any Shemerians are actually able to climb through the caste and move to Pleroma.
- Meaningless Villain Victory: Although Pontius Pilate succeeds in wiping out the Zealots resistance and executing Jessua, he doesn't have long to celebrate it, since the Demiurge soon launches a massive laser towards Kenoma. Pilate tries to evacuate, but Nicodemus kills him because he refuses to relinquish the lance containing Jessua's blood.
- Mercy Kill: In the abandoned facility, the party kills Ruthia, who turned into an archon after years of torturous experiments from the Kenomans and being separated from her son. Her transformation is so thorough that Jessua cannot turn her back.
- Messianic Archetype: Jessua is a double subversion. At first, he's an All-Loving Hero who wants to use his powers as the Monad's messiah to save the Shemerians, and wants to make peace with the Pleromans. His name not only sounds like Jesus, his mother is named Mary. Most Shemerians see him as a Hope Bringer due to him healing the sick and wounded. However, experiencing the collective memories of Pleroma's victims causes him to go mad and use his powers for vengeance, showing that he cannot bear the sins of humanity. Worse yet, Nicodemus reveals that Jessua's powers aren't truly supernatural, but the result of alterations to his Somanites, which are nanomachines. After he dies and becomes a ghost, Jessua regains his desire to save both races and uses whatever time he has left on the mortal plane to hold off the Demiurges' laser, all in an attempt to save anyone who cannot evacuate the planet. He also reveals that his Somanites were altered by Hashem, who is ambiguously divine, and while that makes him powerful, it doesn't make him invincible or incorruptible.
- More Despicable Minion: General Herod is the most despicable and sadistic of Pleroma's leaders, outside of Nicodemus, who isn't even really on their side. While the others are cruel, they show some care for their people, but Herod is a Bad Boss who bullies and sexually harasses his underlings. He was also the most brutal of them during the Time of Tribulation, and went as far as to sexually assault Lena in front of Judas For the Evulz. Pontius Pilate states that the only reason Herod has his position is because he's too valuable of a fighter to get rid of, and if it weren't for that, he would send Herod to be experimented on in Sanctuary.
- Nice Job Breaking It, Hero!: In the endgame, Judas realizes that Jessua's aggressive attacks on the Pleroman leaders will inevitably end in failure and massive backlash, so he and his father Joseph sell out the Zealots rebels' location in the hopes of negotiating peace with Pontius Pilate. Unfortunately, too much damage has already been done, so Pilate breaks his promise and not only executes the rebels, but launches another Time of Tribulation as collective punishment on all Shemerians, regardless of their involvement with the Zealots.
- No Good Deed Goes Unpunished: A previous High Baptist, Zechariah, discovered the Pleroman scientists' cruel experiments on David, a boy with Kenoman, Idinite, and Cainite ancestry. He freed the boy from captivity and brought the latter to Shemer, and was executed as punishment.
- One-Time Dungeon
- Mount Ararat is a one-time dungeon, due to the Demiurge destroying it with an earthquake after the player beats High Baptist Caiaphas.
- General Herod's office building and the Pleroman power plant are one-time dungeons due to them being behind enemy lines, making them impractical to revisit.
- Permanently Missable Content: Once the player starts the attack on Pleroma in Chapter 8, they lose access to the Azar Arena and its prizes for the rest of the game, due to the red Azar being destroyed in that battle.
- Point of No Return: Once Judas talks to Joseph in Chapter 11, the player is locked into the endgame with no way to return to any previous area, due to the Zealots being wiped out by the Pleromans and much of Nazareth being destroyed.
- Pragmatic Villainy: The Pleromans perform their atrocities in the name of defeating the Demiurge, which strangely hasn't resulted in the Demiurge retaliating despite their usual penchant for collective punishment. This is because the government is secretly being manipulated by Skylar's Cult, a pro-Demiurge faction, who secretly send Shemerians to the Kingdom of Heaven so that the Demiurge can sacrifice them for power. Once Skylar's Cult is wiped out, the Demiurge decides to slaughter both the Pleromans and Shemerians, since they can no longer reap human sacrifices from the population.
- The Quisling: Keyx is a Shemerian who willingly became a slavemaster in order to get into Pleroma's good graces, even if it means persecuting his own people.
- Rebuff the Amateur: Lazarus and Simon initially reject the party's pleas to join the zealots, since they're just a bunch of young adults with little combat experience. When the party points out that the zealots have too few members to do anything against the Pleromans, the zealots agree to let them on the team, but only after they prove their combat ability.
- Red Herring: The game makes it seem like Judas will end up pulling a Face–Heel Turn or becoming more radicalized in fighting the Pleromans, since his name is the same as the biblical traitor and he has a grudge against Pleroma. In a twist, it's the Jesus analogue, Jessua, who becomes radicalized, with Judas fearing what his friend is becoming. While Judas does betray Jessua and sell out the Zealots, he did so in the belief that doing so would prevent bloodshed between the Shemerians and Pleromans, not realizing that Pilate was going to kill all the Zealots and collectively punish Shemer anyways.
- The Revolution Will Not Be Civilized: The Zealots initially seem like a wholly benevolent rebel group, but when it comes time to raid Pleroma, they kill civilians in order to weaken the country, which shocks Judas because he idealized the resistance.
- Rewarded as a Traitor Deserves: Keyx betrayed his fellow Shemerians by becoming a slavemaster working for the Pleromans. The Pleromans take away his status and trap him in slavery under the brutal General Herod when he loses control of the Azar Manufacturing Facility.
- Sole Survivor: In the ending, Lena is the only party member to escape the Demiurge's attack on Kenoma by piloting Kaphar and using it to escape to Idin.
- Straw Misogynist: According to Nicodemus, General Herod sees women as his toys, and he uses his authority to sexually harass female government workers. Worse yet, he's revealed to have sexually assaulted Lena.
- Stupid Evil: In the endgame, Lena nearly beats General Herod to death and only stops because of Judas's pleas to not give in to her vengeance. Just as she walks away, Herod gloats about raping Lena during the Time of Tribulation, and Lena responds by unloading an entire clip into him.
- Taking the Bullet:
- Jessua takes a fatal hit from an archon while protecting Lena. Fortunately, Hashem awakens Jessua's power as a messiah and revives him.
- Lazarus dies protecting Jessua from one of Herod's Azar pilots. Unfortunately, this leads to Jessua gaining the memories of those who were killed by the Pleromans, causing him to become a mad avenger who escalates the Zealot rebellion to suicidal levels.
- Unskilled, but Strong: Like Joshwa in the first game, Judas, Lena, and Simon gain control of three cutting-edge Azar mechs, but have no training in piloting them. As such, they can dominate experienced pilots who have weak, mass-produced Azars, but struggle more against pilots who have similarly advanced Azars.
- What the Hell, Hero?: In the endgame, Jessua suffers Sanity Slippage and turns the Zealots resistance more violent in order to attain vengeance against the Pleromans. Hashem tells him that his power as the messiah is meant to serve others, not to be served, as a not so subtle way to say that he's using his messiah status as a way to achieve his own personal vengeance than to truly save people.
- Would Hurt a Child: The Pleromans aren't above experimenting on children, and they subjected Ruthia's son, David, to painful experiments that traumatized him for life.
- Would Not Shoot a Civilian: Judas wants to rebel against the Pleromans, but is against attacking civilians. Unfortunately, his fellow Zealots are willing to kill civilians both out of vegeance and to weaken the Pleroman government, much to his dismay.
- You Have Failed Me: The Pleroman council demotes and enslaves Keyx after he loses to the party and allows the slaves at the Azar Manufacturing Facility to escape.