OK, you have to go south from the 7th gym city until you find some Dive water. Dive and follow it to a cave. Go inside and emerge in front of the submarine. You can now proceed to kick the butt of Team A/M.
Then go back into Rune City (8th gym), on the left side, go to the top. You'll be led through this cave where you catch Groudon or Kyogre. NOW the gym will be open.
- Mark Ericson