Yes, you know the Phoenix layout, but in this battle it's far mroe complex than ever. There are suddenly laser beams to redirect and doors that you could not get through before. Also, the weapons vendor is by the entry now so you can easily get weapons before you head into battle.

Finally you get to the bridge, and everyone is OK. The disk has a complete copy of Nefarious' battle plan. It's recharging on Koros right now, so you have to get it there.

Ratchet and Clank 3 - Up Your Arsenal Walkthrough