Lysandre/Manga/History/XY

Lysandre makes his first appearance in Professor Sycamore's lab. The professor shows him a video of the battle between and  that happened in Vaniville Town. Lysandre notes from the footage that Xerneas can give life while Yveltal takes it. He asks Sycamore to give him a copy of the footage for further study.

After meeting with Professor Sycamore in Lumiose City, Trevor is sent to Lysandre Café to meet with Lysandre and get his broken Holo Caster repaired. As he and his friends wait for the repair job to be finished, Trevor notices Lysandre's silhouetted figure in a photo of the Vaniville Town incident. Trevor immediately becomes suspicious of Lysandre and fears that he may be behind the attack. Lysandre notices this behavior and asks to see the photo. When Trevor refuses, Lysandre sends his Pokémon out to threaten him. He is stopped by the arrival of Diantha, who uses her Mega to threaten Lysandre into backing off. Lysandre gets a call from Xerosic, who has discovered the tree form of Xerneas at and asks whether or not to begin moving the tree to Team Flare's base. Lysandre hangs up the call and goes to leave on other business. He leaves Trevor's repaired Holo Caster on the desk and bids Diantha farewell. Later, he travels through the skies on top of his. He notes that Gyarados is more excited than usual due to witnessing Mega Evolution with its own eyes. Lysandre assures Gyarados that it too will be able to Mega Evolve as he opens his hand to reveal a Mega Stone.

Later, Lysandre returns to Team Flare Secret HQ after Xerneas's tree form has been successfully transported. Xerosic presents Lysandre with the Lysandre Machine, which he forced a captive Clemont to build for them. Lysandre also receives a Mega Ring fitted with a Key Stone that Celosia stole from Korrina. He then activates the Lysandre Machine and prepares to use it to absorb Xerneas's energy and power the ultimate weapon. Later, Lysandre is interrupted by, who had broken into the headquarters in order to put a stop to Team Flare's plan. Lysandre battles with X and uses his Key Stone to Mega Evolve his Gyarados.

Despite X having three Pokémon capable of Mega Evolving, he does not use it against Lysandre. Lysandre is surprised when his Mega Gyarados is attacked by X's Li'l Kanga, which Mega Evolved in secret by hiding in its mother's pouch. While he watches the two fight, Xerosic notices that the energy used to power the machine is being drained. X reveals that his used its  to pull the electricity into its tail. Immediately afterward, Xerneas awakens from its slumber. Despite the appearance of the Legendary Pokémon, Lysandre is not fazed, as he noticed that Xerneas is in its blue Neutral Mode, which he states is nothing to get worried about.

X's friends and allies arrive at Geosenge Town, where they find the ultimate weapon in the process of being unearthed. The Gym Leaders and Y attempt to stop the ultimate weapon from being activated while Trevor, Tierno, and Shauna head inside the Team Flare Secret HQ to help X. As they make their way to the ultimate weapon's control room, Trevor and his friends meet AZ, the immortal former king of Kalos that Lysandre stole the ultimate weapon's activation key from. They befriend AZ and free him from his jail cell. When Trevor's group arrives at the control room, they find that X has already been defeated.

Upon seeing Lysandre's face, Trevor goes into a rage and fear-filled frenzy and goes to the platform where Lysandre is currently standing. Trevor yells at Lysandre to remove the key, only for Lysandre to suggest that Trevor do it himself. In response, Trevor has his Flabébé blast Lysandre off of the platform and immediately begins attempting to remove the key. Tierno and Shauna go up to assist Trevor, but the weapon is fired despite their success in removing the key. Despite this, the combined efforts of Trevor, his friends, and the Gym Leaders weakened the ultimate weapon to the point where no innocent lives are taken. As he has Xerneas take X and his friends back to the surface, AZ gloats over the heroes efforts to stop Lysandre's ambition just after being captured by Xerosic's.

Although Team Flare blamed the ultimate weapon's blast on X's friends and the Gym Leaders, their efforts did not fool every person in the region. To lay low from the public view, Team Flare relocated to the Pokémon Village. While there, Lysandre begins training with his Pokémon while taking shelter inside of a cave. After Xerosic discovers the stones lining are also another form of the Absorber, Team Flare begins capturing the Pokémon inside the village and has them put on the stones in order to drain their life energy.

These actions gain Team Flare the anger of, the protector of the Pokémon Village. When X and arrive at the village to stop Team Flare, they find Lysandre in battle with Mewtwo. Lysandre manipulates Mewtwo into battling X and Blue so that it may be weakened enough to be captured. Despite having battled together, Blue's attempt to get Mewtwo to recognize him ends in failure. During the battle, Mewtwo attacks X and Blue, but redirects the attack towards Lysandre to hit him instead. Mewtwo then proceeds to Mega Evolve into Mega Mewtwo Y. As Mewtwo battles Lysandre's Pokémon, Blue notices another person in the distance who was responsible for Mega Evolving Mewtwo.

Lysandre retaliates by activating a remote control device to summon Essentia and Zygarde from underground. Lysandre reveals that he had the limiters on Essentia's suit removed, allowing him to fully control her as if she were a puppet. By using a speaker system, Lysandre can speak into the device and have Essentia repeat his words so that he can command Zygarde to attack. The person who Mega Evolved Mewtwo, Blaine, reveals himself and proceeds to assist X and Blue. Lysandre retaliates by having Zygarde attack everyone with, causing heavy damage. The damage dealt to Blaine forces Mewtwo to revert back to its normal state, but Blaine counters by using his connection with Mewtwo to have it Mega Evolve to Mega Mewtwo X.

While Zygarde battles against Mewtwo, X decides to sever Lysandre's control of Zygarde by attacking Essentia. Though successful in breaking her helmet, X is shocked to find that Essentia is actually Emma. Although Emma initially refuses to stop working for Lysandre so that she may pay Cassius for taking her in, X's words convince Emma that what she is doing is wrong. Despite this, Lysandre continues to use the controller to force Emma to control Zygarde. Cassius soon arrives and tells Emma that she doesn't need to work with Team Flare and has his destroy Lysandre's controller, breaking his connection to Zygarde. Now freed, Emma attempts to have Zygarde attack Lysandre, only for his Gyarados to attack her. Lysandre takes Zygarde's Poké Ball, thus making Zygarde his to command. Lysandre has Zygarde attack with another Land's Wrath, causing everyone to be sent flying. Y, seeing that Lysandre was distracted by the attack, decides to take the chance to have her bite Lysandre's hand. Lysandre has Pyroar attack Solsol, but is unable to prevent his Mega Ring from being taken away. Angered at the loss of the ability to use Mega Evolution, Lysandre has his Gyarados blast Y away with.

Despite the loss of his Mega Ring, Lysandre proceeds to make a speech to the entire Kalos region and tells them about his plan to destroy everything with the ultimate weapon. Once Lysandre has finished, X returns with his entire team sent out. X reveals that he borrowed the Key Stones from his allies and uses all five to Mega Evolve five Pokémon at once. Though he is impressed by this feat, Lysandre is unfazed by X's attempt and sends Zygarde to battle X's Mega-Evolved team. The strain of controlling multiple Mega-Evolved Pokémon proves to be too much for X, causing him to be unable to focus on anything other than Zygarde. Lysandre attempts to exploit X's weakness by having his Pokémon attack, only for them to be defeated by Blue's Charizard and Mewtwo.

As X's team continues their attack, X's friends notice that Zygarde's body has begun to break apart. Y's Xerxer reveals that this is due to it and Yveltal returning to their dormant tree and cocoon forms. After Xerxer and Yveltal fully revert, X has his team launch one final combined attack on Zygarde, which causes it to fully break apart. With Zygarde gone, Lysandre begins falling to the ground below him. As he falls, Malva attempts to help Lysandre, but both end up landing onto the sharp rubble below. As he lays in a pool of blood, Lysandre weakly asks the unconscious Malva why the ultimate weapon has not been fired yet.