In Pokémon Omega Ruby and Alpha Sapphire, the Prison Bottle can be obtained through having Hoopa in the party and entering a Poké Mart. A new clerk will show up near the counter at the far left side. If the player interacts with this clerk, the game transitions to another view as the clerk tells the player a story.
After his story, he will give the player the Prison Bottle.
Story of the clerk
"Hey, do you have a minute for a story? This is something that happened when I was watching the store one time... It was, like, a totally dark night. Moonless. And I was all, "No way! This is so-o-o-o creepy!" Then, suddenly—whoosh! Out of nowhere, the automatic sliding door...slides open. And then this super-duper-scary old guy comes in, kinda unsteady, you know? Kinda shambling... So I'm thinking how terrible and scary is this, and then the old guy shuffles over to me... He has a package, like, clutched in his hands... He's mumbling that he has to show it to me... Then he asks, "Do you know what this is worth?" He keeps staring right at me and not even blinking. I was so freaked out. I was, like... "Oh yes. It's, uh, really something, isn't it?" So the old guy grins at me, and he says... "Then I'll just give you this instead of money. Now give me everything you've got in this store!" That's what he said! Really! I was like, "What is this? Too weird, my dude!" But I was scared, so I started shoveling over Potions and, like, whatever I could reach. I gave the dude everything for his stupid package. And out he goes, like, with a wicked grin on his face... As he's walking out, he says, "Three days... For a mere three days will Hoopa be unbound..." Really! I was all, "Stop freaking me out with this nonsense!" I was, like, sweating. The back of my shirt was soaked. Anyway, nothing I could do, so I open the package. It's just a dirty old bottle. Li-i-i-i-ike, really. So I go, "Weirdness. Wonder what's in it." I grab the stopper and carefully pull it loose. Blapt! It popped open, but there was nothing inside! So I figure I totally got fooled. ...Thanks for listening to my story. Know what? I'm gonna give you the bottle from that night 'cause you're so nice. It's not doing me any good anyway. Really."
"Sometimes I wonder if it really is only a dirty old bottle. Those last words that the old guy said as he left... "For a mere three days will Hoopa be unbound..." Just can't seem to get that out of my head..."
"Oh... You're that kid from that time... What did you end up doing with that old bottle? Though...I guess it doesn't matter anymore. Really. It's just, even now, it's still bugging me, you know? "For a mere three days will Hoopa be unbound..." That's what he said. I just can't seem to forget it..."
When used from the Bag on a Hoopa Confined, it changes into Hoopa Unbound for three days.
Hoopa Unbound also changes back to Hoopa Confined when deposited into the PC (prior to Generation VII), when withdrawn from the PC (Generation VII), when deposited into Pokémon Bank, or when deposited in Pokémon Day Care or the Pokémon Nursery.
In the present time, Ghris's great-grandson, Baraz, found the bottle and unsealed it. However, upon touching the bottle, he was possessed by the dark power sealed inside. He then returned to Dahara City and opened the bottle, causing Hoopa to transform back into Hoopa Unbound. This caused Hoopa to go on a rampage once again, prompting Meray to reseal the Unbound power back into the bottle. The bottle was later stolen by Team Rocket, who wanted to get their hands on the power inside of it. This action allowed Hoopa Unbound to possess Meowth and force it to release it once again. With the help of Baraz and Meray, Hoopa was able to resist the dark power from taking over its body.
The Prison Bottle destroyed
However, the bottle then unexpectedly shattered into pieces, and the disembodied dark power formed into its own entity, a "shadow" of Hoopa. Baraz realized that the shadow was formed out of Hoopa's anger of being imprisoned for a hundred years, and it had destroyed the bottle to avoid being sealed away again. Knowing that the Prison Bottle could be remade, Baraz guided Meray, Clemont, Serena, and Bonnie to Dahara Tower, where they used Frogadier's Water Pulse, Braixen's Flamethrower, and a wildHippopotas's Sand Attack to provide the same elements that had been used to create the bottle a hundred years earlier: Water, Fire, and Earth.
The Prison Bottle was successfully recreated, and Hoopa's shadow was sealed inside it. Although the shadow temporarily took over Ash, Hoopa was able to drive away its dark power. This allowed Ash to use the bottle to grant Hoopa the power of Hoopa Unbound in order to save the people of Dahara City from a disturbance in space-time without losing control of itself. Afterwards, Hoopa was peacefully returned to Hoopa Confined. During the movie's ending credits, Meray was seen transforming Hoopa into Hoopa Unbound so that it could help rebuild the destroyed Dahara Tower.