Xenosaga 2 has many settings in which the story takes place. The following is a short overview of each place in my own words.
NOTE: There are very slight spoilers included.
Old Miltia: The center of Miltian Conflict 10 years ago. The game starts in the middle of the Miltian Conflict here with Canaan and chaos. After the Miltian Conflict, the path to Old Miltia was shut off. The Original Zohar was lost here on Old Miltia.
2nd Miltia: After the Miltian Conflict, all city life was moved here. Shion and Jin's home resides in the 8th district. This planet is also a center for much business as the home of the UMN Control Center, Vector's 2nd Division Headquarters, and the traditional Moby Dick's Cafe. Other places accessed while here are the Representative Helmer's office, the waterway, spaceport, water port, and residential/commercial districts.
Subconscious Domain: The Subconscience Domain is similar to the KOS-MOS Encephalon Dive in Episode One. This time, however, it's MOMO's Subconscious that is dived into. Being that MOMO is modeled similar to Sakura Mizrahi, many of her memories are similar to Sakura's as well. It's here where much of the URTV story is exposed. Places visited are the Yuriev Institute, Sakura's home, and a Summer/Winter landscape leading to the beach.
Yuriev Institute: To elaborate, the Yuriev Institute is the home of the URTVs including Citrine, Rubedo, Nigredo, and Albedo. Their father, Dr. Yuriev, treated Sakura's sickness here as well. The Yuriev Institute is only explored during the dive into MOMO's Subconscience Domain.
Elsa: The Elsa has been renovated from its Episode One form. It now has a newly improved UMN terminal, Droid Repair Center, ES Hangar, and even houses the Robot Academy. Like in Episode One, you ride the Elsa almost everywhere you go.
Durandal: The Durandal is the most famous landmark of the Kukai Foundation. It also doubles as an airship typically captained by Shelly and Mary but occasionally by Gaignun or Jr. The Durandal rarely serves as a method of transportation in Episode 2. There are less areas accessible in Episode II than Episode I.
Kukai Foundation: The Kukai Foundation is one of the top ten fastest growing corporations/foundations. After the Gnosis attack from Episode One, the townspeople have been diligently rebuilding their lives here. You can still visit the residential districts and water ports you were able to visit in Episode I.
Dammerung: This ship is where the Vector 1st R&D Division is stationed along with a few other Vector Divisions. While trying to escape, Shion and Allen head into the restricted division in an attempt to retrieve the E.S. Dinah.
Ormus Stronghold: A center of activity belonging to the Immigrant Fleet. This fortress appeared between two black holes blocking the path of the Elsa from Old Miltia. Thus, the party took it down from the inside-out. Here, you fight Richard/Hermann, Pellegri, and Orgulla.
Omega System: The final dungeon. After Proto Omega awakened, it formed a giant fortress around itself called the Omega System. Here there are many strong Gnosis and the final confrontation occurs. There is a section that can only be accessed through the Environmental Simulator, and players get to choose between an E.S. section and a Character section midway.
