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Flagship Whole.png

The Rebel Flagship is by far the most powerful vessel in the Rebel Fleet, and serves as the game's final boss, located in The Last Stand sector.

At The Last Stand, the silhouette of the Rebel Flagship is visible hovering around a beacon, marking its location. Every two jumps you make, it will jump closer to the Federation base, taking a total of 6 or occasionally more turns to reach the base. If it remains at the base for 3 consecutive turns, the Flagship will destroy the base and end the game in a Rebel victory.

Your goal is to intercept the Flagship, fighting through three stages to destroy it and ensure a Federation victory. With each stage that you beat, the Flagship will jump away, nearing the Rebel fleet. It will wait for one turn before jumping back to assault the Federation base.

Global behavior[]

At the end of the first and second stage, the Flagship will lose a part of its hull along with the rooms, systems, and weapons in the corresponding location. Other systems will be installed on the next stage, changing its behavior dramatically.

On the second and third stage, the Flagship has a special ability called "Power Surge" which will be triggered periodically and cannot be disabled by the player, much like Environmental Hazards.

Hull and system damage of the Rebel Flagship will be repaired on the next stage. Breach and fire will also be cleared. Only the crew is persistent through each stage; crew members killed are not replaced on the next stage. If the player jumps away from the Flagship before completing a stage, the same applies, with one exception: the crew is fully replaced if the player retreats during the first stage.

Unlike other battles, killing the entire enemy crew won't defeat the Flagship. Instead, a message will state that the AI took control of the ship. The Flagship will then behave like an automated ship: undamaged systems are treated as manned (even those that are hacked), and damaged systems are all progressively repaired at a set rate, except those with fire or a breach in their room.

The Flagship's "weapons" are artillery systems, each located in its own room. They cannot be manned, despite containing crew. These rooms are also isolated from the main structure of the ship (with an exception on hard mode).

Although the Flagship uses a missile launcher, it does not consume any missiles and will therefore never run out of ammunition.

After the Flagship jumps away, the player will receive a small amount of scrap, fuel, drone parts, and/or missiles. There is also a slight chance for a random weapon or augment being dropped.

If you have a clone bay, any of your crew on board the Flagship can be cloned after it jumps away, unlike any other battles in the game.

The Rebel Flagship limits Sensors functionality capping them at level 2: enemy system power use or weapon charge progress are only available through hacking.

Flagship variation[]

On Easy mode with Advanced Edition Content disabled, the Flagship only has 3 layers of shield instead of the usual 4 (which means the shield system level is 6 instead of 8). This applies for all three stages.

On Hard mode, two additional rooms link the Laser and Missile ones to the main section of the ship. This makes it more difficult to stop the enemy repairing them.

1st Stage[]

The Final Boss, 1st stage (transparent systems only exist when playing with Advanced Edition enabled; transparent rooms only exist on Hard mode)

The Final Boss, 1st stage



Numbers in parenthesis are system levels.



Like any other ship, the Flagship consumes 1 drone part to deploy its hacking drone. This means it is possible (yet difficult) to avoid being hacked entirely by shooting down 10 hacking drones in a row with Defense Drones. However, this approach is very unreliable due to Drone Targeting Glitch (all images) and overall possibility for a defense drone to miss its target; additionally, many other projectiles (including missiles) are being shot at your ship, which can destroy or distract the defense drones. See another approach to handle enemy's hacking.

Dodge Rate[]

Assuming cockpit and engines are unharmed and the engines are fully powered. Based off system health of the engines and cockpit.

  • Base Dodge rate: 10%
  • While fully manned: 20% (Enemy crew is unskilled regardless of difficulty)
  • If unmanned and Piloting room is empty: 8%
  • If controlled by AI: 20%

2nd stage[]

The Final Boss, 2nd stage (transparent rooms only exist on Hard mode)

The Final Boss, 2nd stage

With its cloaking (and hacking) gone, the boss now relies on its drone system along with its power surge, which spawns more drones.


  • Hull: 22
  • Reactor: 44
  • Crew: The remaining crew from the previous stage (Minus the one in the Ion room if left alive).
  • Drone parts: 10

Like on the previous stage, it is possible to avoid being boarded entirely by shooting down the Boarding Drone until the Flagship runs out of drone parts. Since it uses 4 drones at once, this can happen quite quickly.

Note that drones from the Power Surge don't consume drone parts.


Numbers in parenthesis are system levels.

The Boss Ion was lost during the previous battle.


The Hacking, Door and Cloaking systems were lost in the previous battle.


Power Surge[]

The Flagship deploys extra drones, randomly split between Beam and Combat (both mark 1). The number of extra drones depends on difficulty: 4 on Easy, 6 on Normal, and 7 on Hard. The split between Beam and Combat drones remains fixed for every surge, unless you jump away and come back.

The cooldown of the Power Surge varies randomly each time, between 20 and 30 seconds. A warning sounds exactly 5 seconds before the surge begins.

The extra drones will take two shots each and then disappear. As a result, the length of the power surge varies, but is about 7 seconds. If you are cloaked, they will position for taking a shot, and that will count as one of their allowed two shots.

Hacking or destroying the drone system does not affect the power surge drones. They are an independent hazard.

Dodge rate[]

Assuming cockpit and engines are unharmed and the engines are fully powered. Based off system health of the engines and cockpit.

  • Base Dodge rate: 15%
  • If fully manned 25% (Enemy crew is unskilled regardless of difficulty)
  • If unmanned and Piloting room is empty: 12%
  • If controlled by AI: 25%

Final stage[]

The Final Boss, 3rd stage (transparent systems only exist when playing with Advanced Edition enabled; transparent rooms only exist on Hard mode)

The Final Boss, 3rd stage

With its drones gone, the Flagship now relies on its Zoltan shield, power surges, and boarding crew to overcome the player.


  • Hull: 20
  • Reactor: 32
  • Crew: The remaining crew from the previous stage (Minus the one in the Beam room if left alive).

The Flagship's Zoltan Shield has 12 health points.


Numbers in parenthesis are system levels.

The Boss Beam was lost during the previous battle.


The Drone system was lost in the previous battle.

Power Surge[]

  • Shoots 7 laser shots simultaneously, or...
  • Brings its Zoltan shield back online

After every 3 laser Power Surges, the 4th will instead fully restore the Zoltan Shield. The cooldown of the Power Surge varies each time, randomly between 20 and 30 seconds. There is a warning exactly 5 seconds beforehand.

If any of your crew are on board when the Zoltan shield comes back on, they will be stuck and can't be teleported back until the shield is broken again (unless you have Zoltan Shield Bypass).

Dodge rate[]

Assuming cockpit and engines are unharmed and the engines are fully powered. Based off system health of the engines and cockpit.

  • Base Dodge rate: 28%
  • If fully manned: 38% (Enemy crew is unskilled regardless of difficulty)
  • If unmanned and Piloting room is empty: 22%
  • If controlled by AI: 38%

Weapons cooldowns[]

The Flagship weapons are artillery systems, working just like the Federation Cruiser artillery system, but with different base charge times. Damaging the system slows down the weapon. In phase 1 and 2, they have 3 system levels. In phase 3, they have 4 levels.

Charge time (seconds)
System level Ion Laser Missile Beam
1 35 25 28.75 32.5
2 28 20 23 26
3 21 15 17.25 19.5
4 (phase 3) - 10 11.5 -

Recommended upgrades[]

The Flagship has high damage output, especially in phases 2 and 3. Good defences will make the fight much safer:

  • Aim for level 5 engines and 4 shields (3 shields minimum).
  • Cloaking is very useful, for dodging missiles and power surges.
  • Defence drones are less effective, but still useful.
  • Mind control and upgraded doors are helpful against phase 3 boarders.
  • Level 2 oxygen stops a phase 1 oxygen hack killing your crew.
  • Level 2 piloting stops a single hit knocking out all your evasion.

Consider damage buffers to other critical systems too (upgrading them one extra bar, for resilience against a single hit). Good candidates are shields, cloaking, mind control, and weapons.

Strong offence is equally useful. Ending the fight quickly will limit the damage you take. Look for some of the following:

  • Strong weapons that can deal damage through 4 shields, even with several misses
  • Hacking to remove the Flagship's shields or evasion
  • A teleporter to disable the Flagship's isolated weapons
  • A way to kill the main crew in phase 1
  • A way to get through the Zoltan Shield quickly in phase 3

The Zoltan Shield in phase 3 has 12 hit points. It can be taken down more quickly with ion or beam weapons, or combat or beam drones. A Beam Drone Mark II does 2 damage with each hit. Zoltan Shield Bypass can be useful when boarding.

Your offence should not rely heavily on missile weapons, since the defence drone in phase 2 will shoot them down (unless you have a Defense Scrambler). It cannot stop you using hacking, however.

General strategy[]

With a good setup and strategy, it's possible to defeat the Flagship while taking no damage.

See also: beginners' Flagship guide video

Always have a plan for the Flagship, and upgrade your ship accordingly. As you get closer to the end of the game, imagine how your current ship will handle the final battles. Are your defences adequate? Do you plan to kill the crew slowly in phase 1, or will you use powerful weapons to end the fight quickly?

Try to enter the Flagship fight in good shape. You get 10 free repairs upon entering sector 8, and Repair Beacons can patch up your hull for free. Your ship should not be taking much damage from regular fights in sector 8.

In all phases, the Flagship's missiles are a major threat, so have a plan for dealing with them. Your plan could be as simple as "use weapons to destroy the missiles"! The other weapons are much less dangerous, but can be deadly when they sync up with the power surges.

Cloaking can be used to dodge the missiles or power surge attacks. The timing of power surges varies, and cloaking will not always be ready for dodging the next one. Unlike the Flagship weapons, power surges are not delayed by cloaking, so it's often desirable to end your cloak immediately after the surge. This can be done using a level 1 cloak, or firing your (non-beam) weapons to disrupt a longer cloak.

Higher-level cloaking can also be used to dodge both the missiles and a power surge. For example, in phase 3, a level 3 cloak can dodge the first missile volley and power surge (example), while also delaying the next missile volley by 15 seconds. This is not guaranteed, due to the variable surge timing.

With good defences, the missiles are often more dangerous than the power surges. 4 shields and 5 engines is a solid defence against the surges.

Handling phase 1 hacking[]

Phase 1 will use level 3 hacking against you. This can range from trivial to deadly, depending on which system it hacks. The system is randomised each time, so it may be wise to jump away if the Flagship hacks a critical system. Do not jump away if you only have 1 turn remaining before the Flagship destroys the base!

The worst hack targets are usually weapons or shields. Beware using a defence drone to shoot down the hack; this rarely stops all the hacking drones, but it does change the hack timing. If you allow the hack to land immediately, then a shields hack will end before the Flagship can fire its laser or beam weapons.

Perhaps more importantly, an immediate weapons hack will mostly overlap with the Flagship's 10-second cloak. Delaying the hack changes this timing, with the result that you may be prevented from ever firing your weapons! You will not encounter this elsewhere in the game, since no other enemies have both hacking and cloaking.

It's sometimes possible to use a defence drone to selectively block hacks. You can watch where the drone is aiming, and then unpower if it looks like the hack is heading for an unimportant system. This could result in a delayed weapons or shields hack, however!

Handling phase 2 drones[]

You can use a defense drone to shoot down the Boarding Drone. Otherwise, it can be helpful to open internal doors and power your oxygen system to level 2: this will keep oxygen in the room, so your crew can fight it more easily.

If you damage the Flagship's drone system, the Boarding Drone is the first drone to go down. Further damage will take the regular combat and beam drones offline (not the power surge drones), and finally the defense drone.

The power surge drones can potentially deal enormous damage, especially if the laser weapon fires just beforehand. In addition to good general defences, it's useful to have fully-trained shields crew and a Shield Charge Booster. With these defences, you will usually take no damage from the power surge.

Handling phase 3 boarders[]

Unless you kill the crew in earlier phases, phase 3 will board you with most of their remaining crew. The Flagship will also use its level 3 mind control against you. These threats combined can be highly disruptive.

Before jumping to phase 3, you can position crew in unimportant rooms, so that the mind control happens somewhere manageable (example).

You can counter their mind control with your own (level 1 is enough). Bear in mind that enemy boarders will always try to join your mind-controlled crew, and this can be used to your advantage. They will single-mindedly bash down blast doors without fighting your crew, so follow them around the ship for easy crew fights. Even if you have mind-control, you may want to delay using it for this reason. Beware that once enemies are in the same room as your mind-controlled crew, you cannot choose who will be targeted by your mind control! In this situation, you may want to vent your crew out the room to separate them, before using mind control.

As always with boarding defence, proper use of venting is crucial for controlling enemy crew movement and stacking the fight in your favour. You can also use venting to force your mind-controlled crew into a different system.

One highly-effective strategy is to "kidnap" the enemy boarders:

  • After phase 1, wait at the base until the Flagship returns to you.
  • Fight phase 2 at the base, then follow the Flagship when it jumps away.
  • This ensures you have a safe escape beacon (the base) in phase 3.
  • Wait until several enemies have boarded your ship, then jump to the base and kill them at your leisure.

Boarding strategy[]

Easy and Normal mode[]

On Easy and Normal difficulty, all the Flagship's weapons are isolated and vulnerable to boarding. This makes a teleporter very effective.

Phase 1 can be completely neutralised by boarding the weapons with two crew. Board the missile weapon first, then the ion weapon, then the beam weapon. Once these weapons are destroyed, the Flagship cannot damage your ship (assuming you have 3 shields).

You can now take your time killing off the crew in the main compartment. Killing these crew means that the Flagship will have no defence against your boarders in phases 2 and 3, and you will not need to deal with boarders in phase 3.

There are various ways to kill the Flagship crew. You will need to plan around their level-3 medbay:

  • Destroy the medbay with your weapons, then fight inside it.
  • Use your weapons to snipe low-health crew running to the medbay.
  • Hack the medbay to finish off hurt enemy crew.
  • Hack another room to prevent hurt enemies escaping to the medbay.
  • Mind-control enemies, then teleport them back to your ship and kill them there.
  • Set the shields room on fire, and hack the room or mind-control the crew.

It may help to break down doors, giving your crew more freedom of movement. Once broken down, enemy doors will not shut (unless the room is breached).

This strategy is much more effective if you do not kill the crew in the Flagship's laser weapon. Leaving one crew alive means the Flagship will not activate its AI, so any broken systems will stay broken, and the Flagship will have less evasion (the AI gets manning bonuses).

In phase 2, board the missiles immediately with two crew. This will prevent them from ever firing. In phase 3, take down the Zoltan Shield as soon as you can, then board the missiles; a Zoltan Shield Bypass lets you board immediately.

Hard mode[]

On Hard difficulty, the laser and missile weapons are connected to the main body of the Flagship. This makes the above boarding strategy much less effective, since the Flagship crew can contest your boarding and repair damage to those weapons. It also means the main body has two extra crew.

Killing the crew is still possible in phase 1, but you must balance this against the need to avoid taking excessive damage from the missile launcher.

With cloaking, even a single point of damage to the missiles (including ion damage) will allow your cloak to recharge in time for the next volley. The damage does need to come early enough, not immediately before the missiles fire. With both cloaking and hacking, hacking the missiles will allow you to cloak every volley.

With hacking, cloaking, and a teleporter: hack and cloak missiles, while boarding the ion and beam weapons. This neutralises the Flagship's offence. You can then board missiles and gradually kill off the enemy crew, who will have difficulty escaping to the medbay since hacking locks the doors.

Hacking by itself can be an effective way to kill crew, depending on your weapons setup. Hacking shields hampers enemy movement, creates a kill zone, and makes it easier for your weapons to destroy the missiles. Once missiles are down, send some lasers into the shields room. This has a good chance to start fires. Naturally, the Fire Beam and Fire Bomb can be even more effective. Once fires spread, enemy crew will not be able to put them out and will all eventually die.

You can also use mind control to kill enemy crew. Level 2 mind control in the shields room will eventually thin out most of the Flagship crew. Mind control is an effective way to prevent crew putting out fires in the shields, or to prevent them repairing the missile weapon.

When killing the crew, you may prefer to leave one crew alive in the main body of the Flagship, since this prevents the AI from activating. The AI is mostly a minor nuisance, however, and you may also prefer to kill all the crew for uncontested boarding.


After this long struggle, the victory screen appears. It has the name of your ship as well as the names of every crew member that survived the encounter (excluding those who were on board the Flagship when it was destroyed in the final phase if you do not have a Clone Bay). If your ship is destroyed at the same time you destroy the Flagship, it will count as Victory as well.

You will also have the words "Victory" if your ship is a new high score.

Final boss4.jpg
The Big Bad Boss finally bites
the inter-planetary dust
Victory Screen Victory Text