After Cyrus's defeat, while Saturn redeems himself and takes over the business and research aspects of Team Galactic, Charon takes over the criminal aspect and leads an attempt to capture the Legendary Pokemon Heatran. However, Mars and Jupiter ends up deserting, claiming that things were more interesting when Cyrus was in charge, and he is arrested by Inspector Looker.
In the anime
Charon appeared in Saving the World From Ruins!, albeit not in a speaking role. He is seen briefly in Team Galactic's base.
Charon made his first full appearance in Gateway to Ruin! along with Saturn where they were trying to find the Spear Pillar in Mt. Coronet.
Charon made another appearance in Team Galactic's finale from Unlocking the Red Chain of Events! to The Battle Finale of Legend!, where he assisted in the final stages of the Red Chain project. He is not arrested, unlike the other three Commanders at the end of the arc, and presumably escaped.
He appeared briefly in DP191 in Team Rocket's fantasy with all the other members of Team Galactic.
He is often seen with a laptop computer and does much of the technical work for Team Galactic's plans, such as monitoring energy levels and other statistics. Compared to the other Galactic members, he is the most laid back and upbeat, which often causes one-sided squabbles between him and Saturn.
Pokémon Adventures manga
In the Diamond & Pearl chapter, Charon is one of Cyrus's top scientists and is responsible for the creation of the Red Chain. During most of his appearances Charon is either shadowed or has his face obscured by a person or object. It isn't until Cyrus is defeated at the Spear Pillar where he finally makes his first full appearance.
After Cyrus is defeated by the hands of Diamond, Pearl, and Platinum, Charon can be seen watching them from a distance. Charon notes how Diamond has a Regigigas and wishes to steal it from him. However, he is spotted by Diamond and the machine he was holding is taken by the Gym Leader Byron. Unfortunately, Charon's machine causes a disturbance in the hole in the sky that was created by Dialga and Palkia's fighting and mysterious tentacles shoot from the hole and pulls Cyrus, Palkia, and Dialga inside of it. Charon uses the distraction to introduce himself to his captors and escape. As he leaves the vicinity, his notebook detailing the information of Legendary Pokémon is stolen by Diamond's Kit at the last moment.
In the Platinum chapter, Charon is seen with the Galactic Grunts looking for the Legendary Pokémon Heatran. After he manages to trick Buck into uncovering the Magma Stone that seals Heatran in Stark Mountain, Charon steals it and uses it to attack him. When Looker arrives to help Buck, he is forced to defend himself from the attacking Charon and his small army of Grunts. After Looker manages to capture Charon, he begins to question his motives. Charon replies that he is looking for the Distortion World and is capturing the Legendary Pokémon in order to prepare an arsenal to get there.
The aftermath of the battle is unseen but it is seen that Buck and Looker were seriously injured and were sent to hospital after being rescued by Platinum's Pokémon.
Later, Charon arrives in Eterna City after Giratina enters the real world and begins going on a rampage. He appears before Diamond and Pearl and tells them of his plan to capture the legendary and rare Pokémon of Sinnoh. He sends out Heatran to battle the two in an attempt to take Diamond's Regigigas. As the battle continues, Charon forces Giratina to attack Pearl with Shadow Force, but Diamond pushes him out of the way and is hit instead.
With Regigigas's Trainer dead, he tries to convince it to join him, only for it to turn around and leave instead. Charon teases Pearl over the death of his friend, sparking the boy's anger. He tries to attack Charon, but is sent flying by an attack from Charon's Slowking. Despite knowing that he might lose, Pearl decides to attack Charon, shocking him by revealing that he has one of the Pokémon Charon wanted, Rotom.
However, before Pearl can attack, Regigigas soon returns with Rotom's appliances so that Rotom can attack Charon in its rage. Together, Regigigas and Rotom force Charon and Giratina to retreat back into the Distortion World. Later, he encounters the other Galactic Commanders who are angry at him because he doesn't care about Cyrus, and only wants legendary Pokémon.
Charon lies to them by claiming that he is searching for Cyrus too, but his search is impeded by a group of people that were attacking him. He asks for their help and convinces them to fight off the people that were attacking him and they comply.
After Dialga and Palkia are freed from the cage Giratina trapped them in, Charon reveals he has Darkrai under his control as well and sends it and Heatran to battle against the other legendary Pokémon. The battle quickly gets chaotic, leading into a big brawl between ten legendary Pokémon along with an unwilling Shaymin.
The sight of all these Pokémon sends Charon into a giggling frenzy, to which he exclaims that he intends to capture them all. When Platinum tries to stop him, Charon faces her with his Slowking, only for it to lose easily to her Pokérus-infected Pokémon. Disappointed in how an "ordinary" Pokémon fights, Charon abandons his Slowking and goes to the legendary Pokémon, only to see Heatran being defeated by Regigigas again. Charon has Darkrai put everyone to sleep with Dark Void so that Giratina can get in an attack with Dragon Pulse. Shaymin joins in the fight and uses Worry Seed to wake everyone up, allowing everyone to redirect Giratina's attack at Charon, destroying his flying machine in the process.
Charon decides to retreat, and has Giratina fly the both of them out of Distortion World so that he can leave everyone trapped inside. Diamond, Pearl, Platinum, and Shaymin chase after him, but neither are fast or powerful enough to catch up to Giratina, allowing Charon to escape. However, just as he does, Charon and Giratina are greeted to a powerful Draco Meteor used by Cynthia, which defeats them in the process.
Although Giratina is defeated, Charon tries to escape once more in the same way he did on the Spear Pillar, but is cornered by Diamond, Pearl, and Platinum. Charon tries using his machine to control their Pokémon again, and forces them to fight each other. Suddenly, a toy robot crashes down onto the machine, destroying it in the process. When Charon tries to smash it with a boulder, the toy shocks him, revealing itself to be Rotom in the process.
After everyone that was left behind emerges from the Distortion World, Charon tries to lie to Cyrus by claiming that he intended to gather the legendary Pokémon for Team Galactic's sake. Cyrus reaches down to Charon, which Saturn and Mars think it means he's going to pinch him. However, Cyrus only takes the machine, and praises Charon for his technological genius. The records reveal that he has been using it since the battle on the Spear Pillar, which angers Saturn into figuring out that he was attempting to use the machine to control Dialga and Palkia into opening a hole to the Distortion World, to which Charon denies.
Cyrus speaks to his four Commanders once more and reveals that he is disbanding Team Galactic, and takes Mars, Saturn, and Jupiter away with him. Angry, Charon says that since they're bad guys, they should be arrested, to which a faraway voice agrees. The voice is revealed to be a now-healed Looker, who arrests Charon once and for all.