Now that Team Rocket is officially through with Unova, let's reflect on the five distinct missions they undertook in the region, each built up through a number of episodes and conluding with a two-parter. Which is your favorite and why? If you want to mention least favorite, then by all means do. Sorry, no "all of them" or "none of them" options here.
The missions are as followed:
The Meteonite --- 19 episodes. Jessie, James, and Meowth steal energy from the Dreamyard, data from the Antamony Research Center, and a Meteonite fragment from the Nacrene City Museum, all while dealing in secrecy with other agents and avoiding the police. The end result is the discovery of the Meteonite in the Desert Resort, which prompts Giovanni himself to head to Unova. Infamously, this mission's conclusion has been postponed indefinately, but essentially the Meteonite gets destroyed by Ash and Pikachu and Giovanni leaves.
Nimbasa City Subway --- 8 episodes. Jessie and James hijack the Nimbasa City Subway system and terrorize the city's populance with a "ghost train" while Dr. Zager hides out in Anville Town. When Meowth arrives at the Pokemon Center with Ash's group, he steals all the Pokemon, including Pikachu and the rest, and loads them aboard the "ghost train", which heads to Anville Town to rendevouz with Dr. Zager. Only through some surprising Pokemon training skills from Pikachu and overconfidence on Meowth's part does this mission fail.
Milos Island --- 5 episodes. Jessie, James, and Meowth break the seals on Tornadus and Thundaras, causing them to be released and fight each other. To save the island, Ash and his friends summon Landorus to stop the other two Legendary Pokemon. Team Rocket steps in to steal all three, but obviously didn't think a good escape plan through, as the Pokemon are freed from Dr. Zager's helicopter rather quickly, causing Team Rocket to make a retreat, with Jessie vowing they'll recapture those Pokemon somehow.
The Time Gate --- 3 episodes. Dr. Zager has Jessie, James, and Meowth steal superelectric stones from Chargestone Cave and, combining this with data stolen prior to the Nimbasa mission and the dream energy stolen during the Meteonite mission, creates a fossil restoration mission. Reviving a Tirtouga/Carricosta at Twist Mountain, Team Rocket attempts to use it's life force to open the Time Gate in the mountains depths, so that they may amass an army of Pokemon from the prehistoric past. They are defeated and the Time Gate closed.
Operation Tempest --- 11 episodes. Jessie, James, and Meowth locate and excavate the ruined Undella Bay Temple while Dr. Zager uses spying devices to record the song of Meloetta, the Legendary Pokemon travelling with Ash's group. When all is ready, Giovanni arrives in Unova once again and captures Meloetta. With Meloetta and her song in the temple, Giovanni obtains the Reflecting Mirror, which he uses to summon and control Tornadus, Thundarus, and Landorus. The final battle with Team Rocket in Unova occurs......