Cyrus/Manga/DPA

Cyrus is first seen watching a Contest being performed by Mitsumi in Hearthome City. He introduces himself as a friend of hers to Hareta and then leaves after asking Hareta to give her his regards on her performance.

Later, at Celestic Town, Cyrus, Jupiter, and Saturn arrive at the ruins after Hareta manages to throw a bomb they planted into a safe area. Here, Cyrus introduces himself to Hareta as the leader of Team Galactic and reveals that he is also searching for the Legendary Pokémon. After revealing his plans, Cyrus makes his leave while Hareta follows him and Mitsumi is left behind to battle Jupiter and Saturn.

After catching up to him, Cyrus offers to let Hareta join him in his operation; Hareta refuses and they begin battling. The two have an intense battle and eventually, Hareta is knocked off of the bridge they were fighting on and is sent into the water below. Cyrus begins to mull over his victory, but Hareta suddenly returns from the water and defeats his with a -powered. Suddenly, Cyrus realizes that he is starting to enjoy their battle; in a fit of rage and confusion, Cyrus commands his to use, destroying the bridge and sending Hareta into the water once again, this time unconscious. Cyrus then leaves while questioning how he lost control over himself in their battle.

Later, at Lake Valor, Cyrus arrives after Saturn is defeated by Hareta. Disappointed by his failure, Cyrus unceremoniously fires Saturn from Team Galactic and tells him to leave. Noticing that Hareta is still alive after previously defeating him, he is challenged to a battle by the boy and they begin battling. Cyrus almost defeats Hareta again, but he quickly loses his advantage once Hareta sets up a well-planned move. Before his Gyarados can be defeated by a fired from Hareta's, Saturn saves it with his 's  and begs for another chance. Suddenly, Hareta defeats Saturn with a Torrent powered-up Surf from his Piplup; Cyrus takes the unconscious Saturn away and states that their battle was a draw while forgiving Saturn for his loss.

Later, while Jupiter battles Mitsumi at Lake Acuity, Cyrus sends a phone call to Jupiter in which he requests that Mitsumi comes to him. It is eventually revealed that Cyrus had picked up Mitsumi when she was a child and raised her to be Team Galactic's greatest warrior. By holding her beloved hostage, Cyrus forces Mitsumi to once again fight for him and makes her battle Hareta. As they battle, Cyrus coldly tries to convince Mitsumi that she is alone in the world and that she only belongs in Team Galactic. Eventually, Hareta manages to break through to Mitsumi and convinces her to fight as a real Trainer instead of a member of Team Galactic.

After Mitsumi is defeated, Cyrus leads Hareta to the room where he holds the three Pokémon of spirit,, , and. Hareta manages to free them from their prison, but Cyrus managed to complete the item he was creating with the three Pokémon, the Red Chain. Cyrus assumes that Hareta hates him for his actions but is shocked to only find that he pities him instead. Cyrus gives Hareta a Master Ball and tells him to go to Mt. Coronet where they can have one last battle; he then leaves the self-destructing Galactic Building with Hareta still inside.

Later, at the Spear Pillar, after waiting for the return of Hareta, Cyrus assumes he had died in the explosion and goes on with his plan. With the Red Chain, Cyrus finally summons the Pokémon of Time,, and takes control of it. With Dialga's control over time, Cyrus easily defeats Hareta's and he announces his plan to destroy everything to start the world anew. Cyrus commands Dialga to send the world back to its beginning, causing everything revert to the start of the universe. Hareta's Empoleon attempts to sacrifice itself to stop Cyrus, against Hareta's wishes, but is stopped by the lake guardians who save everyone and break the Red Chain, freeing Dialga from Cyrus's control.

With Dialga freed, Cyrus has been defeated, but suddenly, the other god Pokémon,, arrives. While Dialga and Palkia fight, Cyrus witnesses Hareta, Mitsumi, and the Gym Leaders attempt to try to stop them, only to fail. Cyrus states that while the imperfect world will end, nothing will remain to replace it. Mitsumi states that Hareta won't let that happen because he is fighting for all of them. Mars, Saturn, and Jupiter come to help them fight Dialga and Palkia; Cyrus then explains to them how to defeat the two dragons.

Hareta uses Cyrus's plan and manages to get Dialga to use, stopping it momentarily. With Dialga frozen briefly, Cyrus and the others command all of their Pokémon to attack Dialga simultaneously, stopping the fight between the two gods. After the events end, Cyrus disappears along with his commanders. Some time afterwards, Cyrus is captured by Charon, who takes over Team Galactic. When Kaisei accidentally breaks into Cyrus' prison cell in the Team Galactic HQ, he offers to free Cyrus, but Cyrus turns him down, saying that he is waiting to see what Charon plans to do with Team Galactic.

During the battle against Charon in the Team Galactic HQ, Mitsumi and the three Commanders free Cyrus, and they set out to the Distortion World to fight Charon. Cyrus and the others, seeing the battle against Giratina in the forest arrive to assist, and Cyrus is last seen fighting Giratina with the others.

Later, when Charon escapes to Stark Mountain hoping to capture Heatran, Agent Looker stops him, claiming that Cyrus has disbanded Team Galactic.