Complete these missions in either Federation or Klingon campaigns to unlock the indicated ship for use in Skirmish or Multi-Player modes.

Unlock Romulan Frigate:
Complete Mission 3 (Federation Campaign).

Unlock Romulan Destroyer:
Complete Mission 6 (Federation Campaign).

Unlock Romulan Light Cruiser:
Complete Mission 9 (Federation Campaign).

Unlock Romulan Heavy Cruiser:
Complete Mission 12 (Federation Campaign).

Unlock USS Excelsior:
Complete Mission 14 (Federation Campaign).

Unlock Romulan Dreadnaught:
Complete Mission 3 (Klingon Campaign).

Unlock Orion Destroyer:
Complete Mission 6 (Klingon Campaign).

Unlock Orion Heavy Cruiser:
Complete Mission 9 (Klingon Campaign).

Unlock Gorn Light Cruiser:
Complete Mission 12 (Klingon Campaign).

Unlock Gorn Heavy Cruiser:
Complete Mission 15 (Klingon Campaign).

If you want to play as the bad guys then you've got to complete Mission 15 in the Federation Campaign before the option becomes available.

At the Main menu enter the following codes to unlock the corresponding effect, if they have been entered correctly a window will pop to confirm. These codes must be re-entered everytime you start the game.

Unlock ALL Missions:
At the Briefing screen enter Up, Down, Left, Right, Select, Start, Start.

Unlock Extra Crew Upgrades (5 Promotion Points):
At the Crew screen enter Up, Down, Left, Right, Select, Start, Select.

Unlock ALL Ships for Skirmish and Multiplayer:
Up, Down, Left, Right, Select, Start, Y.

In a Mission select any Ship:
Up, Down, Left, Right, Select, Start, B.

Unlock Klingon Campaign:
Up, Down, Left, Right, Select, Start, X.