Plot
Ender Magnolia takes place decades after its predecessor Ender Lilies in the same world. The game is set in the Land of Fumes, where "machine-like artificial life forms" called Homunculi are built to serve the kingdom. These Homunculi have become corrupted from an underground toxic gas, causing them to become violent and insane. The protagonist Lilac is an “Attuner” with the ability to purify corrupted Homunculi. Lilac teams up with a Homunculi named Nola and sets out to rescue the kingdom. [1]
Waking up in an abandoned lab with no memories of her past life, Lilac manages to escape with the help of Homunculi Nola manages to repair her damaged programming with her powers as an Attuner. Nola has damaged memories as well, and decides to accompany Lilac. Upon reaching the surface, Nola explains they much reach the center of the city, the Upper Stratum where the nation's ruling class resides may hold the answers that they are seeking. However, strange "Fumes" that rise from the ground have started spreading Blight and caused Homunculi to lose their sanity and transform into hostile Mutants, forcing Lilac to rely on her Homunculi companions for protection as they journey through Milium's Lower Stratum. Along the way, they recruit additional Homunculi in their party before encountering Chief Attuner Joran, who upon hearing Lilac's story the was rescued by a white haired woman, guesses that she is referring the Attuner Lilia. As Joran attempts to fix the lift that will transport them to the Central Stratum, Lilac learns that Lilia and Nola found her as an infant in the mythical Land of Origin hidden beneath the Lower Stratum, and decided to raise her in secret. Lilac helps repair the lift, and in return Joran tells her everything he knows about Lilia. She was a skilled Attuner who, despite being in line to be the head of House Frost, decided to stay behind in the Lower Stratum to help Homunculi, but has gone missing.
Lilac takes the lift up to the Central Stratum, where she finds that all of the Attuners there have been slaughtered by the nation's administrator, Gilroy, who has become a Mutant. Nola recognizes Gilroy as the Homunculi that stranded her in the Lower Stratum, but Gilroy manages to retreat after he is heavily damaged. As Lilac explores the Central Stratum and recruits more Homunculi, she finds that even the Central Stratum is not safe from the spreading Blight. She heads to an automated factory that continues to mass produce Homunculi that are turning in Mutants to shut it down, but while there also finds a lab where she and Lilia participated in several experiments. There, she encounters Gilroy again, who proclaims his purpose is to maintain the barrier above the city to prevent the Rain of Death from falling on it, and fears Lilac due to her immunity to the Rain since she a descendant of the Ancients, which gives House Frost an advantage. Nola then accuses Gilroy of betraying House Milius, with Gilroy retorting that Nola is the traitor, having been assigned to spy on House Frost but abandoning her mission. Gilroy then retreats, telling Lilac and Nola to find him in the Upper Stratum.
If Lilac decides to proceed directly to the Upper Stratum to confront Gilroy, she learns that the structure that generates the barrier, the Empyrean Parasol, is in fact drawing energy directly from the Land of Origin to power the barrier, and that only specialized Homunculi that Gilroy can maintain its operations. With no other way to stop the barrier from deteriorating, Lilac and Nola challenge Gilroy and defeat him, with Nola remembering that she was also specifically built to manage the barrier. Gilroy reveals he took on the role to protect Nola, as maintaining the barrier causes excruciating pain and suffering. Regardless, Nola takes control of the barrier, and bids farewell to Lilac. However, even when the barrier is restored, it does not stop the spread of the Blight which continues to spread through the Land of Fumes.
Instead of confronting Gilroy straight away, Lilac also has the option to continue to investigate Lilia's whereabouts. She learns that the head of House Frost, Abelia, attempted to transfer her soul into Lilia, but Joran sabotaged the process, taking Abelia's soul into his own body instead to save Lilia. Joran then orders his own Homunculus to kill him to eliminate Abelia for good. Lilac also receives help from a foreign Ancient priestess, who unseals the location in the Land of Origin Lilia is hidden in and helps craft a new Aegis Curio for Lilac to purify the Blight from Lilia. Lilac and Nola successfully purge the Blight from Lilia, and Nola remembers that her true name is Magnolia and that she was Lilia's Homunculus. Lilia explains that while both Gilroy and Magnolia have the power to maintain the barrier, Magnolia also has the power to destroy it. In addition, Gilroy's suffering and anguish is actually corrupting the Land of Origin, spreading the Blight from below and creating the Fumes. She insists that Nola destroy the barrier so they can harness the resulting energy to dispel both the Rain of Death and Blight, though this would also mean the disappearance of magic, which is sustaining both Lilia and the Homunculi. Lilia accepts her inevitable death, while Nola muses that it would finally give immortal Homunculi finite lifespans like humans. After defeating Gilroy, Lilac, Nola, and Lilia go through with their plan to destroy the barrier, purifying the Land of Fumes. With the Rain of Death and Blight gone, Lilac and Nola resolve to live their lives to the fullest with what time they have left.
