After defeating or capturing Kyogre/Groudon, in the first (southeastern/lower left) room of the northern (right-hand) dry corridor, when the player enters the room the message "It feels as though you're being watched" will be displayed. If the player examines the left section of the bookcase in the upper-lefthand corner of the room, they will find a worn report regarding the history of the facility, after reading which the same message appears. Immediately after this, if the player opens a menu such that they cannot see the overworld, upon returning the screen to display the overworld the Odd Keystone appears, enabling the player to battle Spiritomb. The Odd Keystone will also appear if the player saves immediately after reading the worn report and loads that save; in this case, this effectively means that the player cannot continue without battling Spiritomb.
You can catch a Spiritomb in there, do as said above.