Let's see how this shall work:
1. Upon heading to the summit of Mt. Pyre, the two orbs have been stolen, so the old couple gives you the Magma Emblem.
2. Later, you should recieve a call from Brendan/May, telling you that they encountered something funny at the Jagged Pass.
3. Head to the JP (from Mt. Chimney), and walk down. When you get to the middle, the ground will rumble, and an entrance appears.
4. Head inside, and it's the Magma Hideout. Clear your way through, defeat Maxie, and Groudon is liberated.
5. Head back to Lilycove and get to the Aqua Hideout, clear the way, get the Nugget and Master Ball, then leave. The Wailmer should've left by now...