Ratchet & Clank: Up Your Arsenal/Starship Phoenix

This is basically the command center for your missions. It has a VR (virtual reality) battle arena, armour vendor, weapons vendor (with VR testing facility), a VG 9000 game console for playing Captain Quark VId-comics, Bridge, Ship vendor and a trophy room.

Take Qwark to his cage
Once you arrive on the ship, Quark will follow you around. Lead him to your quarters (labelled as "Play Vid-Comic" on the map) and Quark will automatically enter his Cage.

If you have the Bolts, visit the Armor Vendor and buy the Magnaplate Armor for 10,000 Bolts.

You should also visit the VR Deck and finish as many of the training missions as you are able. Each completed mission provides additional bolts.

Meet Sasha on the bridge
Go towards the front of the Phoenix (your ship landed at the back). A cut-scene will begin, at the end of which you will receive the coordinates for Marcadia.

Fly to Marcadia
Go back to your ship and travel to Marcadia.