It's at the Temporal Tower, that's where you battle Primal Dialga,
just note that you would have to bring a lot of Reviver Seeds
and Sleep Seeds because you would be more likely to get knocked out
by Dialga's Roar of Time attack, it only took me 2 trys to defeat him though. ;)
Just keep throwing Sleep Seeds at him, then attack / use an Oran Berry.
Anyway, what chapter are you at the moment? :\