Though this is not part of the Windwaker, this is the third time but as Lana. You start alone but as a twist of fate, you'll be dealing with danger in the desert at all areas of the map.
Gate of Souls dispel
You have to go to where the locations has been marked. It's important to take down Gate of Souls warps by defeating Bilns that act as guardians to stem the flow of enemies.
Tetra and the Helmaroc king
Tetra would be dropped from the top north east corner. She'll come down to the mid-south east area where she'll unfortunately has to fend off from monsters at all angles, including the Helmaroc King. Fortunately, Link comes as well. So switch to Link and have him deal with the giant bird. If you remember back to the Windwaker, use your hammer as soon as the Helmaroc's beak gets stuck in sand. Then attack it as much as you can. The giant bird would eventually go to the Arbiter's Ground to regenerate. You have to defend Tetra until she's clear of the enemies.
At the same time, finish taking down Gate of Souls as Lana as access in the middle has been closed.
Helmaroc King's demise
As soon as Tetra is available to be controlled and there's no Gate of Souls left, get Tetra and Link defending the Allied Base with Lana goes to the north east corner to take over the Arbiter's Ground base. As usual, Lana would encounter enemy reinforcement but they should be easily dispatched. Doing so would keep Helmaroc from coming back and regenerating all over again. All that's left is to defeat the Helmaroc King. Repeat the Windwaker process and the giant bird would finally be defeated.
The cutscene would reveal that the characters has no clue about what to do next. The man with the red clothes and the beard advised them to go search for where Cia would be. By the way, you should also remember "King of Red Lions" that Toon Link talks to as a talking boat and far later reveals to be the king that was trying to help end Ganon's reign.