The Prison Bottle can be obtained after Hoopa is downloaded from the Hoopa event. It can used to change Hoopa into its Unbound form before battle.
The Prison Bottle was once used to seal Hoopa 100 years ago by Baraz's great grandfather.
In Hoopa and the Clash of Ages, the Prison Bottle was used to seal Hoopa Unbound away by Ghris 100 years ago when it went on a rampage. It later appeared again in the hands of Baraz who released the negative energy from it to transform Hoopa into Hoopa Unbound. Meray then used it to recapture the dark energy, only for it to be stolen by Team Rocket, with Meowth being controlled by it in similar fashion to Baraz. Released, the shadow Hoopa attempted to possess the true Hoopa, but upon failing manifested as a separate being. It then destroyed the Prison Bottle, forcing Baraz, Meray and the heroes to craft a new one at Dahara Tower. They succeeded in capturing the negative energy again, and Hoopa was then able to tame its dark side by sharing memories of its time with Baraz and Meray. Hoopa's power was then freed from the bottle so it could save the people who were trapped at Dahara Tower, before being used to contain that power again so that Hoopa could reassume its smaller size.