Seraph Eden is the most powerful of the Seraphim in the Angel World, but there is now a whole new class of angels above her, the Seven Archangels.
Eden first appears in the Ilias Temple Ruins, intruding on the conversation between Luka's party and the Lilith Sisters. She is accompanied by her fellow Seraphim, Zion and Gnosis, and they declare their intent to kill the Lilith Sisters. Eden explains that they come from a world in which Alice I was defeated and the world is now ruled by Goddess Ilias and the Seven Archangels. The three Seraphim and the Lilith Sisters fight, with Eden personally taking on Lilith. The fighting between inhabitants of different worlds causes Sonya to approach.
On the Alice route, Gnosis talks to Sonya only to have her energy and an arm absorbed by the latter. Sonya becomes Sonya Mazda. Lilith says that they must stop this high-level Apoptosis, but Eden refuses to stop their own fight. Luka's party fights and defeats Sonya Mazda, causing her to begin summoning Adramelech. Sonya Mazda drains the dark energy from Morrigan when she tries to intervene, fusing it with the stolen holy energy, and finishes the summoning. Lilith persuades Eden to make a temporary alliance against Adramelech to preserve the world, so the Sisters and Seraphim fight Adramelech together. Luka's party fights and defeats Sonya Chaos, but Adramelech keeps reviving despite being destroyed three times. Eden concludes that the situation is hopeless and decides that she and her fellow Seraphim must retreat from the Paradox world. She advises that Luka's party do so as well.
On the Ilias route, things are initially the same. The Eden of the Paradox world is shocked upon seeing her counterpart. Eden now asks Ilias to wait until they destroy the Lilith Sisters. Morrigan is the one who first has her energy absorbed by Sonya (allowing her to become Sonya Mainyu). Eden declares that she and her allies will stop Sonya Mainyu, only for the Lilith Sisters to continue attacking them. Luka's party defeats Sonya Mainyu, who again summons Adramelech and absorbs Gnosis' energy when she tries to stop her. The Sisters and Seraphim ally against Adramelech and again are unable to permanently defeat her. Eden apologises to Ilias, saying that the end is inevitable once an XX-class Apoptosis appears in a world. The Lilith Sisters retreat but the Seraphim remain, with Eden declaring that they must keep fighting for Ilias' sake. Sonya Chaos reawakens, defeats Adramelech, reverts the damage to the world, copies over a Sonya from another world and disappears. The Seraphim and Luka's party are left behind, unable to remember what has just happened. Eden explains the purpose of her group: to save the chosen ones from other worlds and to slow the spread of Chaos. Luka and Sonya disagree with only saving a few, and Eden admits that they are also uncomfortable with this decision and they'd like to save everyone. Eden then brings up the Lilith Sisters' plan and says that they must devote their efforts to stopping it. She apologises to Ilias for not being able to help her. Paradox Eden reassures her counterpart that Ilias is safe with the former, causing Angel World Eden to praise her counterpart's loyalty. Angel World Eden then says that the party may try to search for another way to save the worlds, but they will inevitably have to resort to the angels' solution. Eden tells Luka that he will eventually have to make a choice and expresses her belief that he will make the "right" choice. Eden tells Ilias that they must depart and asks her Paradox counterpart to take care of Ilias. The three Seraphim disappear into light.
- The Seraphim are now third in power in terms of the angels, following the Seven Archangels and then Ilias herself. In other words, Eden is the first among all thirds.