The story was the guardian colony, Moatoob and Neudaiz are under attack by a unknown race called the seed and you decide to fight them as a Guardian. You later learn Dark Falz has resurfaced and produced those seeds and needs to be defeated to stop his threat on the Gurhal system.
The story was basically a portion of other ideas from the Sega Genesis Phantasy star games. I learned while playing PSU network mode.
girl goes to find new planets on a ship that looks like a cross between a bird and a magical ferris wheel
That's emilia. PSP2 is a continution of where PSU and PSP1 (Vivienne story ends). She lives on Clad 6 working for a Mercanary group called Little Wings.
The planets your mentioned are probably the new maps added to the game. The jungle on Moatoob is a cameo to the Jungle in PSO ep2.
Sega has in-game hints about the ancients and cross-overs but its just for fanbase purposes so it sorta ruins it for people who are trying to make a timeline out of the games. PSP2 hints about the ancient like it did back in PSU but apparently their are forces worse than Dark Falz in PSP2 story.
Sorry, I tried to put a spoiler tag on the vital stuff but I don't know how.