Alright, here's the sequence of events:
1. Do two jobs and talk to Mr. Mime in front of the Kecleon Market. He tells you about the legendary Scizor. You must rescue him from Froslass.
2. Do another job and talk to Sunflora at the Guild. You should then make your way to Surrounded Sea and the Wonder (Manaphy) Egg.
3. Now feed Manaphy two Blue Gummis. The next day, it falls ill and you must retrieve the Phione Dew from Gyarados.
4. Return Manaphy to the sea, do three jobs, and go talk to Team Charm at the Guild's B2F. Search Aegis Cave with them.
5. Now do three more jobs to find that Azurill has fallen into a nightmare and has not waken for days. Scale Mt Travail to find the former outlaw Drowzee, who will send you into Azurill's nightmare.
6. Travese the nightmare to free Azurill, then go talk to Lapras at the beach. That night, you will be taken by Palkia to Spacial Rift.
7. Get through Spacial Rift and defeat Palkia at the bottom. Darkrai will reveal himself and invite you to Dark Crater to confont him.
8. Make your way through Dark Crater with Cressilia's help and fight Darkrai and his minions. Palkia will appear as Darkrai tries to escape through a time hole and stop his attempt. To add insult to injury, Darkrai loses his memory and now appears in five different dungeons.
9. Three jobs later, you will reunite with Manaphy. Three more jobs later, he will tell you about Marine Resort.