Once you're done looking around Waford you can head to the Dust Ruins, to the west of Adio's hut. Adio will use the red orb he found earlier in the game to unlock the door, granting you passage inside. If you thought you were done with fine particulates once you left Alabasta, well... you're not. Clearly.
Save near the entrance, then trigger the cut scene by looking at the sand on the lower platform. Luffy will suggest going back to speak to Lim. Before you leave, check the west side of the railings keeping you from the sea of quicksand. Attached to a wall is a Luffy's Cube Fragment. You need to be hugging the left wall to reach it with Luffy.
Return to Adio's hut. Lim is standing out front, and Luffy will suggest that she send them back into Memoria so you can grab the huge Crab Mover that ferried you around before. This will shoot you back into Nanohana. There's a significant amount of new stuff that you can do in Alabasta before you proceed with the story, so we'll jump to each of the old locations and see what's what.
One thing to note: When you explore outdoor areas you'll now notice that time passes. If you go to a campsite and party you can now choose to rest until morning or until night. You may find different things to do if you go out at night.
Nanohana
- If you climb up onto the building near the gateway that links the north and south of Nanohana, on the south side, you'll find a Memory Link. This leads to a chain of quests called An Evil Deed.
- Check the Spice Bean's Bounty Board and you'll find a new posting for "Land Karate" Rikaon. You can also do this in any tavern throughout Alabasta, though this one's closest.
- Down Nanohana's northeastern street you'll find a man named Pompous Tam. Tam has lost a photograph, and needs someone to get it back. Agree to help to trigger the More Important than Berries Side Story. In the market stall beside Tam you'll find three Sea Pig Meats via Sanji, if you hadn't revisited this area before unlocking his Skill.
- Down the alleyway in the northwest of Nanohana you can find three Gator Watermelons if Sanji is leading the party.
- Head northwest out of Nanohana, towards the desert. Sanji can find three Kung-Fu Dugong Milks in front of one of the stalls on your left.
Great Sandy Desert
- If you explore the southern portion of the Great Sandy Desert you'll run into Leviathans, an enemy that was previously an easy boss. It's... still pretty easy.
- Head to the Sandy Oasis and you'll find a child by the southern bridge. Her name is Mitt, and she needs help from Zoro. Agree to trigger the Night Exterminator Side Story.
- Check the Bounty Board at the Sandy Oasis to unlock four more bounties.
Desert Outside Alubarna
- Check the east side of the Royal Army Garrison and you'll find a man named Segem. He will give you the Battlefield Courier Side Story.
- Cross the bridge between the Royal Army Garrison and the Rebel Army Camp and you'll find a man named Collapsed Jonathan. He desperately needs five Energy Apples. Hand them over and he'll give you five Mighty Excite Apples.
Coming back here also gives you the chance to explore the Rebel Army Camp, which was blocked off the last time you visited:
- There's a Yaya Cube in a barrel along the northeastern wall, beside two NPCs.
- In the middle of the camp is, well, a campsite. Near it is a steel box for Zoro to slice open. It contains an Excite Apple.
- Above the main gate is a walkway that you can access from a pair of ladders. At the north end of the walkway is a chest containing a Banana Gator Pie.
- Along the southeastern wall, right beside the front gate, you'll find a chest containing a Banana Gator Pie. Put Nami in the lead and she'll find 45,000 Berries a short walk south along the wall from the chest.
- Put Sanji in charge and he'll find two Kung-Fu Dugong Milks along the western boardwalk in the rear of the base, near some stacked barrels. Sanji can also find five Sandora Dragon Meats if you steer him to the south end of the boardwalk, beside two chatting men.
Alubarna
- East of the entrance to Alubarna Nami can find 150,000 Berries, beside a cannon.
- In the south of Alubarna you'll find a weeping woman named Lief who will give you the Side Story That Tea Tastes Thorny. (The Side Story didn't appear for me until I'd completed several others in Alubarna, however.) Hidden near Lief, beside a wagon to the north, Sanji can find five Dragon Bananas.
- Nami can find 45,000 Berries beside the stairs that lead into the connective gate passage between the southern and central sections of Alubarna. Check to the east, near a group of three people.
- In the connective gate passage between the southern and central sections of Alubarna you'll find a Collapsed Princess. Give her five Energy Apples and she'll give you a Proof of Helping.
- Northwest of the entrance gate to the Market District Sanji can find five Bo Bo Bird Breasts. They're sitting beside a wagon at the intersection. Down the street to the north of the intersection, along the pillars on your right, you can find a steel box for Zoro to open that contains three Sandy Shells.
- In the southeast of Alubarna's Market District you'll find a small barricade that only Chopper can bypass. On the other side you'll find a chest containing Sandora Dragon Steak Tips. On the other side of a railing to your right Nami can find 45,000 Berries, and Zoro can slice up a steel box to find four Chunks of Meat.
- On the east side of the Market District is a barricade you can bypass by going up and around. Before leaping up you can find four Sazae Kancho Ogre Livers on the ground, if you put Sanji out front.
- Also on the east side of the Market District Nami can find 150,000 Berries. They're on the raised street north of the aforementioned barricade.
- In the northwest of the Market District you'll find an old woman who complains of a bad back. Speaking to her will trigger the Talented Doctor Side Story. Sitting beside the old woman are 45,000 Berries that Nami can sniff out. Later on - and after completing Talented Doctor - you'll find the old woman south of here, and she'll give you the Side Story Dance Rehearsal.
- Check the small plaza in the west of the Market District and Sanji can find three Bo Bo Bird Eggs. They're just south of the fountain, by a cart.
- Just south of the palace is an east-west street that connects to the rest of the Market District. Sanji can find two Sea Pig Meats sitting in front of a stall to the west, and two Kung-Fu Dugong Milks near some packages and stairs to the east.
- In front of the palace you'll find a soldier who is tussling with a familiar camel. He'll give you the Side Story Why Eye-lashes Enlisted. (Though in all likelihood you need to complete The Truth About Eye-lashes before you can undertake this Side Story.) Behind Eye-lashes Nami can find 45,000 Berries.
- Southwest of the palace entrance Sanjia can find five Sandora Dragon Meats. They're sitting near three people staring at a heap of pots and packages, near a gate.
- Beside the General Store to the south of the Royal Mausoleum Sanji can find three Electric Dragon Meats. East of the General Store you can find three Shock Kabuto Meats.
- Beside a cart to the south of the entrance to the Royal Mausoleum Nami can find 45,000 Berries.
Phew. Grabbing and doing everything listed above is hardly compulsary, and most of the character-specific items aren't worth going out of your way, but if your characters start to speak up you might as well change to Sanji or Nami and see what they want.
Head to the Sandy Oasis, in the north of the Great Sandy Desert, once you're done looking around Alabasta for a second time. Travel southeast of the oasis and you'll see the enormous Crab Mover in the distance, on the edge of the sea of quicksand. Lim will decide that it's way too big to bring back to the real world, but Lil' Mover, a crab you rescued earlier, will suffice.
Travel to the Alubarna Royal Mausoleum and descend to B3F. For some reason several Kung Fu Dugongs will follow you. The first, fought by Luffy, is a piece of cake; the second, a stronger Wandering Kung Fu Dugong who's fought by Usopp, is trickier. Use any of Usopp's moves that will burn the thing, consider throwing out a Trick Ball to give it a status ailment, and try any of Usopp's Skills that deal damage to Fooled characters.
Once you're on the broken B3F, use the vines near the bottom of the area to drop into the sand far below. Five Kung Fu Dugongs are waiting, though you can battle them with the whole team so it's not too difficult a fight. Deploy Robin and Zoro for the best results. Take out the Wandering Kung Fu Dugong with Luffy for the best results.
The team will collect Lil' Mover once the Kung Fu Dugongs are out of the way. Use Yoisa Travel to teleport back to Nanohana, where you'll find a Memoria Cube. From this point on you can speak to Lim at campsites, and she will teleport you in and out of Memoria from the Strange Place. So long as the plot allows it, this means that you can return to Alabasta whenever you like.