Due to Aelita oftentimes being critical to the success of X.A.N.A.'s plans, oftentimes, the multi-agent program will attempt to control her. While X.A.N.A. is not normally capable of possessing the Lyoko Warriors sans Jeremie due to becoming immune via their constant virtualizations, the program has access to loopholes. As such, X.A.N.A. usually possesses her by using the Scyphozoa when on Lyoko. As revealed in Wrong Exposure, in addition to brainwashing her, X.A.N.A. also has the Scyphozoa plant an inhibitor inside of Aelita to prevent devirtualization from the terminal, in order to make her accomplish the program's goals without interference. Due to not knowing what would happen if the return to the past was used while Aelita was under X.A.N.A.'s influence (though it was likely that it carried the risk of her being under X.A.N.A.'s control for good), it was not used as a counter-measure.
In Saint Valentine's Day, Aelita was first possessed by a corrupted program chip made by X.A.N.A. and hidden inside a pearl-like necklace she received on Valentine's morning, in the real world. The necklace enabled X.A.N.A. to bypass the restriction of possessing the Lyoko Warriors, as it was not done via a spectre. While under X.A.N.A.'s control, Aelita mainly behaved the same, albeit she was a tad more flirtatious. Once on Lyoko, the Eye of X.A.N.A. was not seen in her eyes but instead on her forehead (similar to William in season 4). After it was made clear that X.A.N.A. was influencing her, Aelita's only impulse was to deliver herself to the Scyphozoa, so that X.A.N.A. could free itself from Lyoko. X.A.N.A. was forced to relinquish its grip once Odd started shooting at Aelita, and back in the real world, the necklace was destroyed.
While under X.A.N.A.'s control during this and other missions in Season 3, Aelita behaved much like X.A.N.A. itself, never talking or showing much emotion besides anger, and, on one occasion, smugness. In addition, any possessions via the Scyphozoa result in the Eye of X.A.N.A. appearing in Aelita's eyes.
In Lyoko Minus One, X.A.N.A. sent the Scyphozoa after Aelita once again, whereupon the monster implanted a mind control program into Aelita, allowing X.A.N.A. to force her to delete the Forest Sector after a Tarantula took her to a way tower. It was revealed that X.A.N.A., knowing that the surface sectors allowed the Lyoko Warriors to counter attacks on the Core of Lyoko, was planning to destroy all of the surface sectors so as to prevent the usage of SCIPIO, as the code was required in order to gain access to Sector Five.
X.A.N.A. was able to possess Aelita again in The Pretender, sending her off with a Manta and a squadron of Hornets, who were able to destroy Ulrich's katana. Despite Ulrich's best efforts, he was not able to stop X.A.N.A. Aelita from deleting the Desert Sector.
X.A.N.A. Aelita appeared again during The Secret, safeguarded by a Megatank, so that she would delete the Ice Sector. However, Yumi was able to stop her, though both girls were devirtualized. It was revealed that doing so would break X.A.N.A.'s control, as Aelita did not show any signs of being under X.A.N.A.'s control afterwards. Unfortunately, this proved to be a temporary measure, as Aelita was forced to delete the Ice Sector anyways in Sabotage so that the Supercomputer would not lose all of its data due to X.A.N.A.'s earlier attack.
X.A.N.A. Aelita was utilized again in Double Trouble, where X.A.N.A sent a Polymorphic Specter to bug the Supercomputer, so as to prevent interference from Lyoko. The tactic proved successful, as X.A.N.A. Aelita was able to delete the Mountain Sector without much trouble.
X.A.N.A. Aelita appeared one final time in Wrong Exposure, where the Scyphozoa brainwashed Aelita so as to fulfill X.A.N.A.'s objective to lure out Franz Hopper. Ulrich attempted to devirtualize her, but X.A.N.A. Aelita proved to be extremely difficult to handle, stealing one of Ulrich's katanas and engaging him in a sword battle. During this time, X.A.N.A. Aelita acted in a fairly deranged manner, walking towards the Digital Sea in a slow stupor one moment, before lashing at her opponents in swift motion, all while sneering and screaming, not unlike X.A.N.A. William. Jeremie was able to use a new program to reboot the Supercomputer, breaking Aelita out of X.A.N.A.'s control, though it exhausted her greatly.
X.A.N.A. Aelita has not been seen since.
Like her non-possessed counterpart, she was voiced by Sharon Mann. In the Spanish, Latin-American dialect, she was voiced by Xochitl Ugarte. In the Spanish, European dialect, dub, she was voiced by Olga Velasco. In Finnish, she was played by Marianna Alanen. In the Japanese dub, she was voiced by Yū Shimamura.
- Saint Valentine's Day (debut)
- Aelita is one of two people who were possessed by the Scyphozoa.
- Despite being possessed the most by the Scyphozoa, it has occurred for the shortest of all Scyphozoa possessions; the only other one being William, who had the longest X.A.N.A.-fication in history.
|Jeremie Belpois | Aelita Schaeffer | Odd Della Robbia | Yumi Ishiyama | Ulrich Stern | William Dunbar|
|Sissi | Jim Morales | Suzanne Hertz | Anthea Schaeffer | Mr. Delmas | Laura Gauthier | Franz Hopper|
|Kiwi | Herb Pichon | Nicholas Poliakoff | Amelia "Milly" Solovieff | Tamiya Diop | Hiroki Ishiyama | Johnny | Takeo and Akiko Ishiyama|
|X.A.N.A. | Monsters|
|Professor Tyron | Ninjas | X.A.N.A. William|
|Jean-Baptiste Pujol | Theo Gauthier | Emily LeDuc | Taelia | Samantha Knight | Samantha Suarez | Heidi Klinger | Mathias Burrel | Magali de Vasseur | Claire Girard | Brynja Heringsdötir | Patrick Belpois | Romain Le Goff|
|X.A.N.A. Aelita | X.A.N.A. Odd | X.A.N.A. Yumi | X.A.N.A. Ulrich | X.A.N.A. Franz Hopper | X.A.N.A. Anthea Schaeffer | Jeremie Clone | Aelita Clone | William Clone | Subdigitals|