Team A.C.T. plays a role in the games as the team that is idolized by the player's partner and Pokémon Square onlookers. They are first seen when Shiftry refuses to rescue Jumpluff's friend due to an unsatisfactory reward; Alakazam tells him that he shouldn't turn down a Pokémon in need, and he grudgingly agrees to go.
When Shiftry doesn't return for several days, the player and partner are asked by Jumpluff to see if he actually carried out the rescue at Silent Chasm. They see that he did rescue the other Jumpluff, but in doing so, he accidentally split a thundercloud with his wind, awakening and infuriating Zapdos. The legendary Pokémon kidnaps Shiftry and dares the player and partner to rescue him at Mt. Thunder. They consult Team A.C.T., who warn them that Zapdos is a very dangerous foe. The player and partner are determined to rescue Shiftry regardless of the danger, so the team agrees to go with them, Alakazam advising that they prepare for a difficult fight.
At Mt. Thunder, Zapdos is defeated before Team A.C.T. arrives at the summit; when it gets back up, Charizard challenges it, but Zapdos states that it is done fighting and agrees to give Shiftry back, praising the player and partner's valor. Tyranitar praises them as well, but Alakazam suspects that the player is no ordinary Pokémon. The partner affirms this by stating that the player is actually a human, much to Charizard and Tyranitar's shock. When asked if he knows why the player became a Pokémon, Alakazam claims to know nothing, but advises them to speak with Xatu at the Hill of the Ancients. However, as the player, partner, and Shiftry leave the summit, Charizard says that Alakazam obviously knows something, and he replies that what he knows about this is better left unspoken for now.
Later, Gengar publicly accuses the player of being the human in the Ninetales legend, claiming that the human is responsible for the natural disasters and must be destroyed to save the world, causing the residents of Pokémon Square to chase the player and partner out. After that incident, Team A.C.T. participates in a town meeting, and while no one wants to believe it, it is agreed that the player must be destroyed. The team approaches the player and partner at their base with the news, and although they seem to be preparing to fight, Alakazam instead tells the player and partner to get away and uncover the truth. He warns them that Team A.C.T. will be among the rescue teams hunting them down the next day, and that there will be no mercy next time they meet.
After the player and partner get through Mt. Blaze, they wonder if anyone else can make it through such a harsh dungeon, only to conclude that Team A.C.T. is more than up to the task, dashing their hopes for rest. Indeed, they are the only team to pursue them all the way through their harrowing journey across Lapis Cave, Mt. Blaze, and Frosty Forest, finally catching up to them at the summit of Mt. Freeze. Sincerely disappointed that the player and partner haven't met Ninetales, Team A.C.T. heavyheartedly prepares to destroy them.
The player and Alakazam briefly clash, but before the two teams can start a full-blown fight, Ninetales appears and orders Team A.C.T. to stop, stating that the player and partner are its guests. Alakazam takes the chance to ask the burning question, and Ninetales conclusively states that the player is not the human from the legend, nor is the human the actual cause of the natural disasters. The partner is visibly elated at this revelation, but angrily yells at Team A.C.T. for wrongfully chasing them down, and Alakazam apologizes for this.
However, the conversation is interrupted when an earthquake happens; Ninetales warns everyone present that Groudon is likely to awaken soon. Team A.C.T. volunteers to quell it, while the player and partner return to Pokémon Square and clear their names. As many days pass with no word from Team A.C.T., everyone begins to worry for their safety, and Shiftry calls numerous rescue teams with the hope of forming a special team to rescue them; Blastoise of Team Hydro, Octillery of Team Constrictor, and Golem of Team Rumblerock volunteer for the role. However, when they end up defeated and expelled from Magma Cavern, everyone begins to panic, exacerbated by Gengar taunting them for facing hopeless odds. However, the player and partner declare their intention to go to Magma Cavern and rescue Team A.C.T., the partner's speech of a rescuer's pride rousing everyone to action again.
Within the depths of Magma Cavern, they find Charizard and Tyranitar, who have been defeated by Groudon. They mention that Alakazam is still fighting it, and the player and partner rush ahead to save him. Further in, they find Alakazam, who warns them to stay back, as Groudon approaches from out of sight. After several thunderous footsteps, the room flashes and Alakazam disappears, presumably defeated. The player and partner are left to fight Groudon themselves, and when the Continent Pokémon is finally defeated, all three members of Team A.C.T. reappear. Alakazam assures them that Groudon will be fine and will no longer present a problem, and they all leave the dungeon. Back at Pokémon Square, everyone congratulates the player and partner for succeeding where all others have failed, and Alakazam states that they have become a first-class rescue team.
However, Xatu telepathically announces to everyone at the square that a falling star, the true cause of the natural disasters, is on a collision course with the planet, threatening to destroy it. The only hope to save the world is to go high above the clouds and convince Rayquaza to destroy the star; all three members of Team A.C.T. agree that the player and partner are the only ones fit for the task. In order for them to be able to go to Sky Tower in the first place, Alakazam assists Xatu in creating the Teleport Gem, and they receive additional help from a Ghost-type Pokémon, who stays hidden and runs off afterwards; Alakazam assumes that said Pokémon is simply bashful. After the falling star is destroyed, Alakazam celebrates with everyone else at the Hill of the Ancients, but is saddened when the player has to return to the human world.
After the player chooses to remain in the Pokémon world, Snubbull finds Luminous Cave and unwittingly evolves into Granbull. Alakazam explains the process and benefits of evolution, as well as the fact that only one Pokémon can enter Luminous Cave at a time. After this, the three members of Team A.C.T. can be found at Pokémon Square. Charizard and Tyranitar are both seen between the Kecleon Shop and Whiscash Pond, wondering about the possibility of higher ranks than Gold. Alakazam sits between Felicity Bank and Wigglytuff Club, and when spoken to, he mentions his role model: the legendary rescuer known as Lucario, whom the highest rank is named after.
After the legendary birds are recruited, and Stormy Sea and Pitfall Valley have been cleared, Alakazam is seen between Felicity Bank and Whiscash Pond. When spoken to, he describes a weather anomaly out in the sea near Legendary Island: a whirlpool stretching to the sky in a massive tornado. This allows the player to speak to the legendary birds at the island, ultimately granting access to the Silver Trench, where Lugia waits.
The day after the player recruits Ho-Oh at Mt. Faraway, Charizard is shown exploring a dungeon, having teamed up with Team Hydro's Blastoise for a change of pace. When Blastoise begins to show his fatigue, Charizard ridicules his reputation as a rescuer, enraging him and encouraging him to prove himself. After the latter fires off Hydro Pump in various directions to show his vigor, Charizard cheers him on, and Blastoise realizes that the Flame Pokémon was just trying to rouse him, thanking him for it. However, the two hear a voice from somewhere, as an unseen Pokémon declares itself to be the strongest in existence before unleashing its power on them. The two arrive at Pokémon Square some time later, barely able to move from their crushing defeat. They warn everyone at the square, including the player, not to go to the dungeon they explored, for fear of facing the brutal opponent that defeated them. This grants the player access to the dungeon in question, Western Cave.
Team A.C.T. joins that player's team after connecting with Whiscash. All are connected with Whiscash.