Pokémon Generations seems to be getting more cinematic every week. This episode sees us delve to the bottom of Hoenn’s ocean to find the legendary Kyogre. While Team Aqua believes they can control the power Primal Reversion, Kyogre has a different idea. Check out the episode below.
See The Power Of Primal Kyogre In The Latest Pokémon Generations

Why is he in primal form? Kyogre and Groudon cannot activate their primal forms before powering up in the Cave of Origins.
Same reason why some of the shorts that has the protagonist there during the events in the games shows them absent like the one here. Loose canon I guess.