This page outlines any ship the player can control in an unmodified game. Enemy ships are outlined on the enemies page. To unlock the second layout (Layout B) of any player-controlled ship, the player must complete at least 2 of three ship-specific achievements. To unlock the third layout (Layout C) of any ship, for those ships that have a type c, the player must reach sector 8 with the B layout of the ship in question. The Crystal Cruiser and the Lanius Cruiser do not have a third layout. All Third layouts require Advanced Edition Content to be on to unlock, and to play.
 Kestrel Cruiser
The player is provided with Layout A of this ship from the start. The ship has powerful starting weapons, but no augments. It's a gunship, with 4 weapon slots and only 2 drone slots. It's designed to blow enemies away.
The type A's burst laser is extremely formidable, accompanied with the three human crew and the Artemis missile launcher the type A is extremely capable in the early game. The type B is capable of tearing through tier one - three shields, but against a tier four, she is useless. The variety of crew allows for dealing with most situations, but upgrades to the lasers are a must to beat the game. The type C starts with dual lasers and an ion stunner, making it worthless against tier 3 and 4 shields, unless better weapons are equipped.
 Stealth Cruiser
To unlock, enter the Engi Homeworlds Sector (Green) with an Engi Crewmember. One of the nodes (Long-Ranged Scanners will show empty space) will have blue dialogue that spawns two quest markers. One quest is a decoy, the other will give the player an additional quest marker. At the new quest, destroy the Mantis ship to unlock the Stealth cruiser.
 Mantis Cruiser
To unlock, enter the Mantis Homeworlds Sector (Red) with a Crew Teleporter and a Med Bay level 2. One of the beacons (Long-Ranged Scanners will show a ship) will have an encounter with a famous thief's ship. Defeat the enemy ship's crew, leaving the ship intact. Select the following blue options after successfully defeating the crew:
- (Teleporter) Quickly send additional crew to look for survivors.
- (Adv. Medbay) Quickly teleport him back to the medbay.
KazaaakplethKilik, the famous thief, will join your crew for saving him. He proceeds to provide you with the plans for the Mantis cruiser and a quest point (in next sector) for a hidden stash of military goods.
 Engi Cruiser
To unlock, the player must simply reach Sector 5. This can be done on any difficulty with any ship.
 Federation Cruiser
To unlock, defeat the Rebel Flagship at Sector 8 with any layout of the Engi Cruiser
Can also be unlocked by defeating the unfinished Flagship in the Rebel Stronghold Sector.
 Slug Cruiser
To unlock, go to the Slug Home Nebula (Purple) with either a Slug crewmember or Sensors level 2. Fight Slug ships at various flight points and damage them to the point of surrender. They will offer you their cargo, and after accepting their surrender there is a random chance that they will offer you an experimental weapon. Ask for data instead and you will see a new quest marker on the map. At the quest marker, the player should first follow the ship by choosing 'Tail the ship'. For the next dialogue, use the blue option to trigger a fight with the fleeing ship. Defeat the ship or kill the crew before they jump to unlock the Slug Cruiser.
 Rock Cruiser
To unlock, enter the Rock Homeworlds (Red). One node will have dialogue insulting your mission. Respond with the "or die trying" option, which will give the player a quest marker. At the quest marker, simply wait for the Rock ship to jump out, and then follow (Do not kill the Rock Ship, let it get away). There will be a new quest marker on your map. Travel there to unlock the Rock Cruiser.
 Zoltan Cruiser
To unlock, enter the Zoltan Homeworlds (Green). One node will have a peaceful dialogue -- respond with "Hear them out" to receive a quest marker. At the quest marker, choose "Attempt to hail" the rebel attacker, then choose the peaceful dialogue options to unlock the Zoltan Cruiser. The peaceful options are the first "Perhaps there could be a reconciliation of our ideals without war?", and then the second "True progress can only be achieved without bloodshed".
 Crystal Cruiser
To unlock this ship, called the Crystal Cruiser, the player must find a Stasis Pod in a derelict asteroid (Long-Ranged Scanners will show a distress beacon and maybe an asteroid field). This event can be encountered in Engi, Pirate, or Rock Sectors at a distress beacon. It is NOT in a Rebel, Mantis, Civilian, or Zoltan Sectors. Rock Plating provides a blue option that guarantees retrieval of the stasis pod (If you're using a Rock Cruiser).
Next, go to a Zoltan or Engi (Green) sector and find the "crew study" event to unlock the Crystal crew member (Long-Ranged Scanners will show empty space). The event is guaranteed in Zoltan Sectors but can also be found in Engi Sectors.
The player must then travel to the Rock Homeworlds (Red) sector and find the Crystal Beacon at the quest marker, which the Crystal crew member will activate using a blue option. The player will be sent to the secret sector, Hidden Crystal Worlds. From there, a quest marker will indicate where the Crystal Cruiser is docked. You unlock the ship automatically on arrival.
This is a hard ship to unlock because all these events must happen in order, and it's very often that they will fail to do so thanks to the random maps. If you get the pod or crew member too late, you likely won't get a Rock Homeworld. Even if you get them early, you might still not even have a Rock Homeworld on your map to go to. You can also easily fail to find any of the spots inside the maps that actually progress the quest.
 Lanius Cruiser
The Lanius Cruiser is unlocked when you have four ships unlocked other than the starting Kestrel. The Lanius Cruiser can only be used when Advanced Edition Content is enabled. This is due to the starting weapons and features using the update's technology.