Pokeman 7:
Destiny Deoxys
(2004)

Deoxys and Rayquaza's fight ends up causing the security bot to malfunction and it starts multiplying rapidly, threatening to consume LaRousse City. Ash and Tory make their way (with difficulty) to the central part of the robot and scan Tory's passport, resetting it.

Rayquaza and the two Deoxys forget their quarrel and go on their way, while Tory ends up adopting Minun and Plusle.

Thanks Mark I!