mayb do some rescue mission untill they ur parther ask u to go groudon in magma cavern and u have to defeat groundon and then u nid to kill rayquaza and u will complete the story but theere is more dungeon waiting for u good luck

Until another team consisting of Blastoise, Occtillery and Golem goes down. Keep doing more missions, and then you get to go.
Link all your moves when you face Groudon.