Lotus was assigned to kill Aria, the empress before Cygnus. In turn, Lotus was fatally injured by a vengeful Phantom, who had fallen in-love with Aria. Lotus was then placed into stasis located deep within Verne Mine, although his soul is separated from his body and can possess other people.
In the present day, Phantom encounters Lotus's ghost and he is found trying to erase the Heroes' existence from history, as well as possessing Wiz the Librarian and Mu Young to attack Phantom. Later, Phantom finds Lotus' body inside a large tank at the power station in the Black Wings' base and attempts to finalize his revenge once and for all, but Lotus immediately possesses him afterward, mocking how Phantom had fallen into his trap and states the strength of his possession ability is based on the distance from his body. Lotus then takes Phantom's body to Ereve in an attempt to assassinate Cygnus, but Aria's spirit appears momentarily and chases Lotus away. Before Aria disappears, he tells his lover not to continue his revenge.
Gelimer eventually came up with a solution to revive Lotus from his state of stasis. However, Lotus remains silent to Orchid's delight; Gelimer reveals to have disabled his brain, leaving only his body and power functional to serve as the scientist's tool. Under Gelimer's command, he attacks his sister in a frenzy and leaves his for dead, though he was picked up by the Resistance.
A hologram of Lotus called "ESS" is now at Gelimer's Evolution Lab. It's a device which allows people to enter Evolution System.
Gelimer eventually launches his plan: Black Heaven, a gigantic airship fitted with massive weaponry all controlled by Lotus. While looking through Orchid's memory to find out what Black Heaven is, it is revealed that Orchid and Lotus were originally spirits before the White Mage gave them bodies and name, in exchange for helping him with his goal. The Maple Alliance forms together to stand against the threat; meanwhile Francis and Orchid also arrive intending to confront Lotus.
The player eventually reaches Black Heaven's core and defeats the possessed Lotus, and Orchid's arrival returns him to his senses. Lotus says that his spirit wandered the world and tried to call out for his sister but the calls were unanswered. he also mentions that he felt emotion when Gelimer forced him to attack Orchid, and wishes to stay human. Gelimer, enraged that his plans have been thwarted, presses a button that gravely injures Lotus. Before he dies, he gives Orchid the remainder of his power and tells his to live, which he uses to destroy Black Heaven's weaponry and thwart Gelimer's plans for good.
- Lotus and Orchid are the names of two flowers.
- Xenon is given the appearance of Lotus when male and Orchid when female, separately from the option to Xenon's own style.