The player is tasked with hunting down a total of 8 Archangels hidden in
Mer-Line stations throughout New Wirral. There are a total of nine Archangels the player may encounter, however, meaning that the last of these Archangels will provide no additional clues via Morgante's song. Every partner character's personal quest, except
Barkley's and
Sunny's, leads the player to an Archangel boss as part of their quest. During this fight, the partner will unlock the ability to fuse with the player. However, despite being fought as an Archangel during
Felix's partner quest
Don't You Want Me,
Shining Kuneko will not unlock an additional part of Morgante's song upon defeat. The remaining five Archangels can be fought with any character at any time, and will feature no scripted events during the battle.
After each Archangel battle, Morgante will appear in a vision, reprising her song, with another of its bars added to the lyrics. The initial two lines of the song are audible immediately after the fight against the wounded Morgante, while the remaining 8 lines are sequentially added as each Archangel is defeated. Morgante's song varies on each save file, though there are a limited number of places the final station may be hidden. Her song will vary in whether she instructs the player to fly to the east or west, and whether to go to the northmost or southmost quadrant. She will also describe the area's appearance (ex. "dark grass" or "crisp snow"). Lastly, she will directly inform the player what actions must be taken, and around what landmark. If the extra Archangel boss is defeated, Morgante will reprise her completed song, and the quest marker will highlight the exact tile on the map that the song gestures towards. Morgante will reprise her song upon the extra Archangel's defeat, even if the save file has already been cleared.
Every time the player defeats an Archangel, Aleph suddenly arrives, absorbing the wounded opponent into his glass head. While his name and motives are initially a mystery, Aleph gradually takes more interest in the player as they defeat more Archangels. After 4 Archangels have been defeated, Aleph awaits the player at Harbourtown, where he properly introduces himself. After the player informs him that their mission is to leave New Wirral, Aleph absorbs them into his head, transporting them to the Dead World. Here, the player is rescued by Ms. Amber, who informs the player of Aleph's history and goals. She then sends the player back to New Wirral. Aleph will continue to absorb defeated Archangels beyond this point, expressing frustration that the player has returned to meddle with his plans. Shining Kuneko is the exception to all aforementioned Aleph cutscenes; she is not absorbed by Aleph after her battle, and defeating her does not contribute to the number of Archangels that must be defeated before Aleph sends the player to the Dead World.
Eventually, the player discovers the entrance of Night's Bridge Station by tracking down its location and performing an action to open the entrance based on the clues and instructions given by Morgante's song. If the player discovers the mirror to Night's Bridge Station before Aleph casts them into the Dead World, interacting with the mirror will display the text "Huh, a mirror...?" Once the player has escaped the Dead World, partner characters may hint while resting that the mirror they discovered could function like a portal akin to Aleph's head. The player is free to enter Night's Bridge Station at any point in the quest beyond the Dead World sequence, even if fewer than 8 Archangels have been battled.
At the conclusion of the storyline, Aleph will summon any Archangel he previously captured during the quest, eventually deciding to fuse with them to become
Aleph Null. Aleph Null's design will accessorize itself with components of the Archangels he fused with. After defeating Aleph for good, he is slain, albeit temporarily. The player may speak to Ms. Amber to perform the game's end credits, which will also unlock additional save file modes. The player may return to their completed save file to continue playing. The Land of Confusion quest will continue to count as an uncleared mission.
