Alphamon is a servant of Yggdrasill.
It first appears in "Reunion" via flashback in which it defeats Motomiya Daisuke, Inoue Miyako, Hida Iori, and Ichijouji Ken in the Digital World. It makes a brief appearance in the Real World when its hand appears through a portal at Haneda Airport to destroy a Kuwagamon that was about to land a finishing blow on Garurumon. It later emerges fully in the Real World to pursue Meicoomon, easily overpowering the Chosen Children's partner Digimon until Yagami Taichi and Ishida Yamato form Omegamon. Alphamon summons its Ouryuken and proceeds to fight Omegamon. The two Digimon are easily matched, but Alphamon retreats back to the Digital World via portal just before it could be hit by Omegamon's Garuru Cannon.
Alphamon briefly appears after the Reboot in "Confession" fighting Jesmon in the newly reformed Digital World. The Chosen Children are caught in the crossfires of the battle. The Children manage to flee as the fight between the two Digimon move away from them, leaving the result of the battle left unseen.
In "Coexistence", Alphamon emerges into the Real World, having been ordered by its master, Yggdrasil sends Alphamon to capture Raguelmon. Alphamon interrupting the fight between Jesmon, Raguelmon, and the Chosen Children. In the resulting battle, it reverts all of the partner Digimon, except Omegamon, back to the Baby II level with just one attack, and fights with Jesmon and Omegamon. Alphamon tackles Jesmon as it fires its Un Pour Tous, forcing the blast to miss Raguelmon, and disappears while the Chosen Children deal with the gigantic fissure that the attack cut in the ground.
While it doesn't appear in "Our Future", it is implied to still be at large after Yggdrasill is shutdown.