From Bulbapedia, the community-driven Pokémon encyclopedia.
Team Rocket HQ (Japanese: ロケットだんアジト Team Rocket Hideout) is the center of Team Rocket's operations. It is located in Kanto, and is where Giovanni and his secretary reside.
During the Indigo League arc, Team Rocket HQ was located in an area populated with trees, apparently within close proximity to Pallet Town. In Showdown at the Po-ké Corral, Mewtwo escaped from and destroyed the building; this scene also appeared in Mewtwo Strikes Back.
After the old base's destruction, the new Team Rocket HQ was located in the middle of a rocky terrain. In The Scheme Team, Jessie, James and Meowth are assigned there. In The Thief That Keeps on Thieving!, the base is shown when Jessie sent the Yanma she caught to Giovanni as a gift, only for him to send it back due to having recently received a large supply of them. In Memories are Made of Bliss!, the base is shown when the Team Rocket trio receive a special mission from Giovanni via Matori.
The HQ appeared in In The Shadow of Zekrom!, when Jessie, James and Meowth were assigned their mission in Unova. The building was shown with a new look. In Enter Iris and Axew!, it was revealed that Jessie and James had left their Pokémon behind at the headquarters. It also appeared in The Dream Continues!, where Jessie and James gave Giovanni their Unova Pokémon and rejoined with Jessie's Wobbuffet.
In It's Mr. Mime Time, Team Rocket HQ was a large tower with some balconies and struts, with the Team Rocket logo being prominently displayed at the base. Its roof acted as a landing area for various aircraft, such as Team Rocket's Meowth balloon.
In Showdown at the Po-ké Corral, Team Rocket HQ was located in an area populated with trees, apparently within close proximity to Pallet Town. It had a central tower with four turrets and red coned roofs on top of each turret, mounted with a satellite dish. It had at least two wings with blue, domed roofs.
In It's Mr. Mime Time, a reception area was shown which had a very lavish design, including red carpets and curtains, busts of a Gyarados statue, a small step, purple polished walls and polished blue tile floor, two fancy potted plants, and a lowerable TV monitor for Giovanni to use to communicate with his underlings when he himself is too busy to meet them in person.
In It's Mr. Mime Time, a room containing various computer consoles was seen. It also had a balcony above it. This room was used to hold Mewtwo when he was not on assignment for Team Rocket.
In Showdown at the Po-ké Corral, Mewtwo escaped from and destroyed this building.
Advanced Generation and Diamond & Pearl
After the old base's destruction, the new Team Rocket HQ was located in the middle of rocky terrain.
In The Scheme Team, the front entrance was shown to possess at least four doors, and also had a two-barred gate with the Team Rocket logo prominently displayed.
The full building was seen in The Thief That Keeps on Thieving! and Memories are Made of Bliss!. The base is a lavender complex with two wings, one on each side, that each have two towers on each end, one of the towers possessing a domed roof. The central building was seven stories tall and had at least two flat trapezoid edges jutting out, with the angled portions containing square bumps. The Team Rocket logo was prominently displayed at the top of the central building. The building was mounted with a set of communications arrays, including two communications satellite dishes and an antenna.
Giovanni's office was a massive room with a red carpet, a potted fern plant, a purple office desk, and a row of windows with blinders on them. The double doors into his office were adorned with the Team Rocket logo. Giovanni had a pencil holder, a lamp, and a laptop capable of scanning the contents of a Pokémon to identify the Pokémon inside (similar to a Pokédex).
Best Wishes and XY
In the Best Wishes series and XY series, the Team Rocket HQ appeared in a new design, still in rocky terrain.
It was a towering complex, being at least nine stories tall, and having two shield-like protrusions on the corners. It was mounted with a series of antennas. There was also a domed building in close proximity. Parts of the HQ may have also been built into the rocky terrain, as some of the mountains were shown to have windows similar to that of the main building.
Pokémon kept in Team Rocket HQ
In storage at HQ
Previously stored at HQ