Omega Alpha Adventure 16 (Episode 16) is the 2nd chapter of Pokémon Adventures: Volume 3 (ORAS).
With Rayquaza at their control, Ruby and Norman go back to Hoenn. Emerald, however, is searching for Sapphire and encounters Maxie and Archie, who decide to stir more trouble. Rayquaza passes by and stops the battle, but it turns on Ruby and throws it away. Fortunately, Ruby is saved by an old friend, whom he helped a long time ago.
Pyramid King Brandon contacts Palmer, who is in Sinnoh, watching a show with his son and his friend. Brandon admits what's going on and tells what's going on, causing Palmer to order his child and his friend to stay indoors today. Brandon reminds Palmer of the rocket crash from Mossdeep City, for Brandon and the rest of the Frontier Brains have battled some strange people. The strange people are Shelly, Tabitha (who growls in pain), Courtney and Matt, all who are asked about Zinnia's location, but they do not know. Suddenly, Salon Maiden Anabel hears a voice and turns to Pike Queen Lucy, who said no word. Emerald, through Hoopa's ring, greets Anabel and asks if Sapphire is around. The Frontier Brains deny she is here, so Emerald has Hoopa close the portal, thinking Sapphire could be in Mossdeep City. Emerald speaks the words "Sapphire" and "Space Center" and Hoopa creates another ring, as Toma-Toma watches. They find a Secret Base, inhabited by a man.
The man wakes Sapphire up, admitting he went to Fortree City to heal her Tropius. Sapphire tries to stand up, but the man reminds her she did fall hard into the water. The 25-year-old man is Aarune, who is from Unova and is traveling around to find Secret Bases. Aarune admits he was with a young man, who created the base at Route 120. The boy wanted to move out and, as they were walking away, he and Aarune found Sapphire, who had fallen down. Suddenly, Aarune and Sapphire hear a noise, which Sapphire is recognizing. She stands up and sees Emerald bickering with Hoopa, both who are glad to see Sapphire alive and well. Before Emerald can reply, a strange noise is heard, as Emerald, Hoopa, Toma-Toma and Granny encounter Primal Groudon and Primal Kyogre. Maxie and Archie appear as well, admitting Primal Groudon has learned Precipice Blades and Primal Kyogre the Origin Pulse. Both think it would be nice to try them out on these people. Hoopa, however, starts moving the rings.
Norman asks if Ruby's fine, who confirms the Jade Orb had managed to control Rayquaza. Rayquaza sees Primal Kyogre and Primal Groudon through the ring. This startles Rayquaza, who throws Norman off its back and launches an attack, through the ring. The attack goes through and nearly hits Primal Groudon and Primal Kyogre. Toma-Toma, Granny and Emerald are shocked to see Rayquaza approaching, though Granny demands something to be done, else a terrible battle will start. Hoopa uses another ring, causing Rayquaza to cross through the first (to Meteor Falls) and right through the second one, elsewhere. Outside the Secret Base, Aarune and Sapphire see an attack, and, immediately after, Rayquaza itself. Sapphire notices Rayquaza is holding Ruby. A boy approaches Aarune and Sapphire. Ruby, however, notices he is at Mt. Chimney and asks of Rayquaza to go to Route 131.
Rayquaza, however, throws Ruby away, who starts falling down. Ruby thinks this is his end, since Rayquaza is refusing his help, since it does not think Ruby can save the planet. Ruby fears he won't be able to apologize to Sapphire. Suddenly, Ruby falls on an Altaria, while the boy is thankful he arrived in time. The boy is Wally, who is standing on his Magnezone. Ruby is surprised to see Wally, who followed Rayquaza from the Secret Base, suspecting its power is needed to stop the meteorite he heard of. Wally chases after Rayquaza and has Magnezone use Discharge. Rayquaza dodges and fires a beam, but misses. Instead, Magnezone uses Zap Cannon, damaging Rayquaza, surprising Ruby, how Wally has gotten stronger. Regardless, Ruby stops the fight and holds the Jade Orb. Ruby approaches Rayquaza, knowing it can Mega Evolve, but it lost its partner and cannot Mega Evolve. Ruby asks of Rayquaza to take Ruby as its partner to solve the crisis. Rayquaza flies to Ruby and gently touches him, pleasing Ruby Rayquaza has accepted his offer.
Just then, Sapphire appears on Troppy and faces Ruby, demanding answers from him.
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