In the games
Jupiter appeared in the Diamond/Pearl/Platinum versions of Pokemon. She was battled by the player on the top floor of Team Galactic's base in Eterna City after she stole some Pokemon. When defeated, she left as Team Galactic were already finished in Eterna and told the player that this was their last warning to stay out of their business.
She then appeared at Lake Acuity, successful in capturing the legendary pokemon Uxie. She had already defeated the Player's Rival, tells him he's weak and leaves.
She was then seen at the Spear Pillar along with Cyrus and Mars when they resurrect Dialga and/or Palkia and attempts to stop the player from interfering with their final plan. The Player's rival arrives looking for revenge and they team up in a double battle against Mars and Jupiter and win.
In Platinum, she only made one last appearance and that was in stark mountain. She along with Mars submissively followed Charon for his own plans to bring Team Galactic back to power. She battles the player after Mars and, after being defeated, learns that Cyrus is gone for good and leaves Team Galactic along with Mars, looking to go on her own journey. It was also shown her that she has a dislike of both Mars and Charon, similar to Jessie and Cassidy's rivalry.
In the anime
Jupiter made her debut appearance in Double Team Turnover! where she was the one to get the Lustrous Orb back from Team Rocket after they stole it from the Celestic Town Historical Research Center.
She was later assigned by Cyrus to lead the capture squad for the Lake guardians, along with some assistance from Pokémon hunters.
She also had a cameo appearance in Saving the World From Ruins!.
Jupiter's first major appearance came in Unlocking the Red Chain of Events!, where she was protecting Charon at the Fuego Ironworks while he was working on the Red Chain. She successfully captured Looker, Jessie and James and later encountered Ash and his friends for the first time. During their encounter, she noted her disgust that Mesprit, Azelf and Uxie had chosen Dawn, Ash and Brock as their protectors rather than herself, Saturn and Mars. With the help from her Skuntank, Jupiter and Charon were able to make a clean getaway.
Jupiter was present when Team Galactic's plans came to a head in The Needs of the Three! where she battled the gang again. In The Battle Finale of Legend! she was asked to guard the outside of Spear Pillar however she was quickly captured by Cynthia and was later arrested, along with Mars and Saturn.
Pokémon Adventures manga
Jupiter first appears in Lake Acuity, where she attacks Platinum, Candice and Maylene, promptly defeating and overpowering them despite their best efforts. She then succeeds in capturing Uxie and delivering it to the Team Galactic HQ and joins up with Mars and Saturn, where the three are greeted by an elated Cyrus. In the final battle at the Spear Pillar, she is defeated and knocked unconscious by Candice and Maylene, who are happy to have avenged their previous loss. Later, Jupiter and her teammates are discovered by another member of Team Galactic, Sird. Jupiter introduces Sird to the others, who in turn explains to them that she had infiltrated Team Rocket on a mission, but failed. Soon after, they are attacked by Riley of Iron Island, who had tracked Sird by her Aura. Sird battles Riley, allowing Jupiter, Saturn, and Mars to escape unharmed.
Later, Jupiter and the other Commanders witness Charon battling Diamond and Pearl at Eterna City with Heatran and Giratina. While the others are irritated that Charon has revealed his true loyalties, Jupiter completely ignores it so that they can enter the Distortion World and rescue Cyrus. After arriving, they find Charon there as well. He lies and tells them that he is searching for Cyrus too, but is being attacked by a group of people and asks for their help.
Believing his lie, Jupiter quickly rushes into battle and they each face a different opponent in a one-on-one battle. Jupiter faces Marley in battle, while Saturn faces Mira, and Mars faces Cheryl. Jupiter proves to be a powerful opponent for Marley, but with information from Platinum, Marley manages to figure out her opponent's Natural Gift tactic.
The battle is interrupted by Giratina, who flies past them so that it can fight the other legendary Pokémon in the area. After Charon is defeated, Jupiter, her fellow Commanders, and Cyrus emerge from the Distortion World and into the real world. Charon tries to lie to Cyrus by claiming that he intended to gather the legendary Pokémon for Team Galactic's sake.
Cyrus speaks to his four Commanders once more and reveals that he is disbanding Team Galactic and prepares to leave. Jupiter, in an outburst of anger, yells at Cyrus for abandoning them because she, Mars, and Saturn will have nowhere else to go without him. Hearing her wishes, Cyrus takes Jupiter, Saturn, and Mars away with him and thanks Diamond, Pearl, Platinum for their help.
Jupiter, like fellow commander Mars, has cruel and spiteful tendencies, making her something of a sociopath (in the games at least). However, she keeps her cool and is fairly level headed (unlike Mars). She also seems to be something of a strategist as she taught her Pokemon TM moves for dealing with weaknesses.