Trainer Tower

This mode features regular one-on-one battles. If the tower is cleared within the target time players will receive an Up-Grade.

This mode features only Double Battles. If the tower is cleared within the target time players will receive a Dragon Scale.

This mode features three Trainers that must be fought consecutively, each with one Pokémon. If the tower is cleared within the target time players will receive a Metal Coat.

This mode features a combination of the battles seen in the other three modes. If the tower is cleared within the target time players will receive a King's Rock.

Trainer	Pokémon
Hiker Mike Reward: N/A	Charizard♂ Lv.1-100 Scope Lens
Crush Girl Rebecca Reward: N/A	Nidoqueen♀ Lv.1-100 Silk Scarf
Black Belt Nicolas Reward: N/A	Poliwrath♀ Lv.1-100 King's Rock
Trainers with a Vs. Seeker by their names, when alerted for a rematch using the item, may use higher-level Pokémon.

The prizes that would be received for clearing each mode are items that can be found elsewhere in the game, and if the Bag is full, the prize will not be accepted.

In Pokémon Adventures, Trainer Tower is a Team Rocket base controlled by R (Japanese: ｒ), a computer created by Carr. It is equipped with 3D projectors, different sorts of weapons, and a restraint system that is almost completely immune to all kinds of Pokémon moves.

Trainer Tower first appeared in Some Things Are Better Left Unown, where Sird contacted Giovanni after defeating Lorelei. Sird retrieved the Ruby and the Sapphire from the tower before heading to Five Island, where the Deoxys named "Organism No. 2" was currently located.

In Once More into the Unown, R held Professor Oak and Green's parents captive in order to lure Red, Blue, and Green to it. After being insulted by Blue, R angrily attacked him and held his Pokémon off. However, Blue had his last Pokémon, Porygon2, infiltrate its network from the inside and shut it down with Zap Cannon, freeing Professor Oak and Green's parents.

After Giovanni succeeded in trapping Mewtwo with the M2 Bind restraint armor, R came back online to explain its use and prevent Porygon2 from moving with a virtual lock. As it gloated, Giovanni noted that it was created by Carr, which explains its rude, crass, and arrogant personality. He then left the building to rendezvous with the Team Rocket airship, leaving the Pokédex holders to battle Organism No. 2's duplicates.

Eventually, Red, Blue, and Green freed Mewtwo from the M2 Bind by using their starter Pokémon's ultimate attacks: Frenzy Plant, Blast Burn, and Hydro Cannon. Like they had planned, these powerful attacks were able to break the armor that R had claimed to be immune to any kind of Pokémon attacks, and then cancel each other out before they could reach and hurt Mewtwo. Once freed, Mewtwo used its spoon to slice the tower in two, destroying it and trapping the Deoxys Duplicates inside.

In Bested by Banette, it was revealed that Ultima, who had come to fight Team Rocket as well, had stolen some items that the evil team had been keeping at the tower, including the Old Sea Map and an ancient manuscript about Jirachi.