When Hoopa Unbound was attempting to capture its true self, Ash Ketchum implored Hoopa to summon some fast Pokémon to help. In response, Hoopa called upon Rayquaza, Latias, and Latios, who proceeded to attack and evade Hoopa Unbound. However, the dark Hoopa countered by summoning forth six other Legendary Pokémon; Palkia, Primal Groudon, Dialga, Primal Kyogre, Giratina, and Kyurem to aid it in defeating the heroes. The trio allied with Ash and the true Hoopa proceeded to undergo Mega Evolution, with Mega Rayquaza employing its enhanced powers against the enemy in such bold moves as tackling Giratina head on.
It later used Twister in an effort to prevent Hoopa Unbound and its minions from reaching Dahara Tower and preventing the recreation of the Prison Bottle, but was overcome by the superior numbers and power of its enemies. Fortunately, Hoopa Unbound was captured and subsequently calmed using the Prison Bottle, freeing the Pokemon it had enslaved. A time-space rift resulted from the actions of the two Hoopas in summoning so many Legendary Pokemon, and Rayquaza attempted to help stop it but was unsuccessful. Following the escape of all those imprisoned by the rift and its closure, Rayquaza joined its fellow legends in departing for home.
As shown in Hoopa and the Clash of Ages, this Rayquaza can Mega Evolve and is a very skilled fighter. It has very developed dodging skills, avoiding Giratina's Shadow Ball even from point blank range and facing members of the Creation trio almost without taking any hit.
It was show to be very brave, shown as it fiercely fought Kyurem that not only have a double type advantage with the Ice-typing, but also have a type advantage through the Dragon-typing and, quoting directly from Iris in Kyurem and the Swords of Justice, is "The most powerful Dragon-type in existence. " . Despite being exposed to it's 2x weakness against ice (Not 4x because Delta Stream was active) once both Rayquaza and Kyurem fell in the sea and the water was instantly frozen, Rayquaza showed determination and great endurance breaking through the tick ice layer and shooting an Hyper Beam at Kyurem.
The Creation trio, Groudon and Kyogre from the Weather trio and Kyurem from the Tao trio all seemed under an powerful mind control from Shadow Hoopa Unbound. It's supported by the fact that, once Hoopa Unbound was contained, all the summoned legendaries stopped attacking. But, even without being updated about what had happened prior to their summoning or why had they been summoned, Rayquaza, Latios, Latias and Lugia still seemed extremely eager to help. So, it's not know if Rayquaza's great colaborativity was product from Hoopa's summoning or if it's a natural trait.
An matter 100% apart from Rayquaza's colaborativity is Rayquaza's obedience. Is not know if it's also product form Hoopa's summoning, but Rayquaza obeyed without hesitation every single one of Ash's commands. In case it's a natural trait, it would either show that Rayquaza is wise enough to recognize Ash's competence as a trainer and let itself guide for it, or that Rayquaza is actually insecure of it's own strategy concepts, choosing to let Ash with the strategy and quick thinking.
It is not known if Rayquaza's amazing display of teamwork is a consequence of the two traits aforementioned, and consequently caused by Hoopa's summoning, or it's a natural trait. In case it is, it would show that Rayquaza have a very good sense of teamwork, working fine for a common objective and covering Latios's and Latias's weaknesses in mid-battle. This display was perfectly showed when it used a combined move with the aforementioned duo, combining it's Twister with two empowering Psychs and acting as a humongous fast rotational shield.
|Hyper Beam||Hoopa and the Clash of Ages|
|Dragon Ascent||Hoopa and the Clash of Ages|
|Dragon Pulse||Hoopa and the Clash of Ages|
|Twister||Hoopa and the Clash of Ages|
|+ indicates this Pokémon used this move recently.*|
- indicates this Pokémon normally can't use this move.
This Rayquaza is the only Legendary Pokémon in the film it appears in to appear different in its normal form from previous incarnations-such as the Rayquaza from Destiny Deoxys due to its Shiny appearance.