The Rebel Flagship

The Final Boss

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

You start in a sector with multiple systems being taken over by the rebels. Jumping to these starts a battle with a tough Rebel Elite ship.

In addition, the silhouette of the Rebel Flagship is visible hovering around a system. Every couple of turns, it will jump closer to the Federation base, and if it gets too close, the game will end.

Your goal is to make it to the Flagship, and fight through its three stages to destroy it, and end the Rebel advance.

With each stage that you beat the rebel flagship will jump away, closer to the fleet. This means that if it is only 1 jump away from the fleet but you have only knocked it down to round 2 you will not be able to defeat it before it reaches the federation base. However, if you knock it down to stage 2 and it is jumping to your base the same time as you are, you are still able to fight. If you FTL jump out of the battle at this stage, though, you will lose.

Contrary to popular belief, it is safe for your ship to FTL jump away from the boss at any time; the only danger is that this may allow the Flagship to get into the unwinnable situation described above. Depending on the map, you may be able to flee once or twice.

In each stage of the fight the boss has a different special ability.

1st Stage

Weapons

Each weapon has its own compartment, meaning if you are boarding the ship, you will have to do so four times, or use missiles.

The Final Boss 1st stage

• Triple Ion Cannon
• Heavy Burst Laser
• Triple Leto Missile Launcher
• Big Beam Weapon (2 damage)

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% (22-30% if enemy crew has pilot/engine skill, assuming that's even possible)
• If unmanned 5%

Systems

• Drones (unused during 1st stage)
• Teleporter (limited and very rarely used during 1st stage)
• Cloaking
• Shields (4)
• Medbay
• Door Control
• Oxygen Control
• Engine
• Cockpit
• Sensors

System Health (IE how much damage a system can take before being destroyed)

• Weapons 3 each
• Drones 1
• Teleporter 2
• Cloaking 2
• Shields 8
• Medbay 3
• Door Control 3
• Oxygen Control 2
• Engine 2
• Cockpit 3
• Sensors 2

Special Ability

• Level 2 Cloak

After the Mothership jumps away, you will receive a small amount of scrap, and fuel, drones, and/or missiles. Also there is a slight chance for a random weapon or augment being dropped.

2nd Stage

The Final Boss 2nd Stage

The boss now uses a Defense Drone I as well as an Anti-Ship I and a Beam Drone I. Drone Control goes from level 1 to level 8, and the engine gets slightly more powerful.

Weapons

• Heavy Burst Laser
• Triple Leto Missile Launcher
• Big Beam Weapon (2 damage)

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% (27-35% if enemy crew has pilot/engine skill, assuming that's even possible)
• If unmanned 7.5%

Systems

• Drones (Laser, Beam, Defense, and Boarding)
• Teleporter (Unused During Stage)
• Shields (4)
• Medbay
• Oxygen Control
• Engine
• Cockpit
• Sensors

System Health (IE how much damage a system can take before being destroyed)

• Weapons 3 each
• Drones 8
• Teleporter 2
• Shields 8
• Medbay 3
• Oxygen Control 2
• Engine 3
• Cockpit 3
• Sensors 2

Special Ability

• Deploys three extra laser drones and three extra beam drones for around 5 seconds. These appear even if the drone control system has been destroyed.

After the Mothership jumps away, you will receive a small amount of scrap, and fuel, drones, and/or missiles. Also there is a slight chance for a random weapon or augment being dropped.

Final Stage

The Final Boss 3rd Stage

The boss now has a Zoltan shield that absorbs more damage than a regular Zoltan shield. Also, the weapon systems gain one more point or level and the engine doubles.

Weapons

• Heavy Burst Laser
• Triple Leto Missile Launcher

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% (40-48% if enemy crew has pilot/engine skill, assuming that's even possible)
• If unmanned 14%

Systems

• Teleporter
• Shields (4)
• Super Zoltan Shield (12 bars)
• Medbay
• Oxygen Control
• Engine
• Cockpit

System Health (IE how much damage a system can take before being destroyed)

• Weapons 4 each
• Teleporter 2

• Shields 8
• Medbay 3
• Oxygen Control 2
• Engine 6
• Cockpit 3

Special Ability

• It can either shoot around 6 laser shots, or bring its Zoltan shield back online. 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.

Victory!

The Big Bad Boss finally bites the inter-planetary dust.

Finally, after three of the toughest fights in the game the Rebel Flagship has been destroyed!

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.

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

Victory screen.

Recommended Equipment

FTL is less strict than most roguelikes, as far as the equipment required to beat the last boss goes. Still, when you get to the Rebel Flagship, you absolutely must do two things:

• Not die, and minimize the risk of dying
• Destroy the Flagship, even if it takes a long time

These upgrades help you to fight the last boss while minimising any kind of risk:

• At least three layers of Shields
• At least level four Engines
• A way to damage the Flagship hull through its shields
• Max skills
• A full eight crewmembers
• Level 2 Doors to control fires and boarders
• A counter to missiles: This is the key point, and can be done in many ways. Most of the Flagship's weapons can be endured with a strong shield and high evasion, except for the missiles. If they hit your shields, weapons, engine, or pilot systems, and you don't have redundancy, it may be necessary to jump out and repair.
  • Cloaking is a nearly perfect counter to missiles or superweapons to dodge them, and gives time to perform repairs so that you don't need redundant levels for damage buffer. However, it costs 150 scrap, and is unavailable to Federation Cruisers. Moreover, the 20 second cooldown usually means you will be vulnerable every other volley: the missile system must be destroyed before the second salvo. Note that since you are dodging periodic attacks of short intensity, level 1 is all that is needed with good timing.
  • A Teleporter can slowly disable all the Flagship's weapons without needing ammo. By prioritizing the missile system you should only take a few hits. However, you won't be able to use the boarding crew for repair and defense on your own ship. Less effective in round three when the Zoltan Shield will block sending and retrieving crew.
  • Defense Drones to block missiles and Boarding Drones. If you don't have one or a couple combat specialists, the constant Boarding Drones will be huge trouble. Be aware Defense Drones can miss (expect at least one Boarding Drone to make it through), and cannot hit all three missiles the Flagship fires in a salvo.
  • Redundant levels and a good repair crew: a Level 3 Pilot subsystem prevents a missile from knocking out all evasion. This is the least proactive strategy to cope with missiles, and it won't stop your hull from eventually collapsing.
  • For the first two stages, a Fire Bomb or better yet, a Breach Bomb are great ways to take out the missile launcher. The Fire Bomb will injured the gunner, cause a fire which may injure the gunner further, and the gunner will be too busy with the fire to man the launcher which slows down the launcher by up to 2 seconds. You will need multiple Fire Bombs to kill the gunner and destroy the missile launcher. The gunner can’t heal which makes all damage permanent.  A Breach Bomb will either destroy or nearly destroy the missile launcher in one hit, heavily injure the gunner, and it will cause a breach. The gunner will need to seal the breach before fixing the missile launcher, which will buy time to get a second bomb ready that can finish off both the gunner and the launcher.

Augmentations

Some Augmentations are not as useful end game as others. Consider swapping out economic Augmentations, like Drone Recovery Arm, in Sector 6, 7 and 8 for more offensive/defensive Augmentations, like Automated Reloader or Shield Charge Booster.

It is important to have your augments synergize well with each other, your equipment, and your strategy for the Flagship fight. For typical fights, a balance works great such as having both an Automated Reloader and a Shield Charge Booster, but in the Flagship fight, 2 Shield Charge Boosters works better in most cases. The Weapon Pre-Igniter is great for typical fights, really helps to get to the Flagship, and even helps taking out the Zoltan Shield in the 3rd stage of the Flagship fight, but it is largely useless in the 1st and 2nd stages. However, when the Weapon Pre-Igniter is paired with 1 or even 2 Breach Bomb Mark II's, Fire Bombs, or a combination, now you can delay (if gunner is still alive) or even take out the missile launcher at the beginning of the fight. Defensive strategies are not the only option. Three Automated Reloaders are especially devastating in the 2nd and 3rd stage if they are paired with 3 or 4 Laser Burst Mark I/II's (L.B. M1= 3.96 seconds; L.B. M2 4.32 seconds to reload). It can even be helpful (though not without risk of prematurely ending the fight too soon) in the 1st stage by either taking out the missile launcher or the medbay quickly.

In the Flagship fights, consider how helpful an augment is and odds that that an augment will help you. Rock Plating gives you slightly better than a 1 in 7 chance of saving you from hull damage. but you still suffer system and personnel damage. You might find Engi Med-bot more helpful since your away teams will heal faster, the rest of your crew will need less micromanagement, and it will be insurance in the unlikely event that a boarding drone or boarding party get on your ship (Flagship boarding drones sometimes make it through when 1 drone is up; could possibly get through 2 drones since drones do miss on occasion).

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

Possible Strategies (Easy Difficulty)

• If you are using the Federation Cruiser, you will need to upgrade your artillery beam; at level 4 this beam is devastating as it ignores all shields and can be recharged quickly.
• Pick up two laser weapons at least, as well as a missile/bomb based weapon, preferably Pegasus (two missiles can be useful in later stages).
• Make sure you have the maximum amount of crew that you can hold and you are ready to fight the final boss.
• Don't delay in engaging the flagship; although there are some profitable encounters on the last map, taking too much time lowers the number of repair spots and time available to visit them. Since you have to fight three stages you can't wait until the last second.
• IMPORTANT: Do NOT kill all of the crew members, only those on the main guns. If you do kill all of the crew an aggressive AI takes over and periodicaly repairs all of the systems that are damaged (similar to the Auto-Scouts except faster). A different approach to this is to leave the gunner just to the left of the cockpit alive, and kill the entire crew before going to the next phase. However, if you are relying on fire damage to win (not recommended) then you do not want to leave this crew member alive as he cannot put out the fires, and repair damaged sections, which you will need repaired in order to deal more damage to the hull. This makes taking out the drone bay and shields practically a joke as your crew will go unchallenged into every room after the first stage. DO NOT attempt this without first destroying their (level 3) med bay unless using crystal crewmembers and their lockdown ability.
• IMPORTANT: If you do manage to kill the crew it does make the last stage of the boss much easier as you only need to worry about the super weapon. As for the aggressive AI, there are two ways to overcome the rapid repairs. One, use breach weapons. Like the AI ships, the flagship can't auto repair any system that has a breach in it. Two, it is easy to overcome at this stage with fire weapons as the damage from the flames is more than the AI's repairing rate, and fire also has a chance to spread causing futher damage to the ship without having to deal with the shields. Though until their shields are down beam weapons, with the exception of the Federation Cruiser's artillery beam, are useless and with the crew dead you're free to target the shields with Bombs and Missiles.
• In the first stage, teleport two crewmen onto the weapon directly to the right of the cockpit. This will take out the triple Leto missile launcher, the most dangerous weapon. Then take out every other weapon one by one. Once you have taken down all of the weapons power down the teleporter as you won't be using it until the next round.
• While your away teams are doing this you can start shooting for the shields; however, with a massive 4 points of shielding and a decent chance of dodging your attacks it is a tough nut to crack. If you have missile weapons you can easily bypass the shields and free up your laser weapons to tear it apart.
• Once you have defeated it for the first time you should try and visit a repair station to heal your ship. If a repair station is unavailable, you can use a hull repair drone to fully heal. It doesn't even need to be active during combat; just swap it in after you've beaten a boss stage and use it at your leasure.
• In the second round it is vital that you take out the weapons at the start again. Its super attack is a deadly swarm of drones that can tear apart any unshielded vessel in the 5-10 second period in which they remain on screen. However, with its weapons out of the picture, level 3 shields should be enough to survive. Before his weapons are down you can cloak to avoid the drone swarm - note that if you allow a L3 cloak to run its full length, it will recharge too slowly to avoid every wave. Decloak early, use Level 1 cloaking or take down the weapons. Then you will have to take out either its shields or its drone control, as its Defense Drone will take out any missiles that you shoot in this round (except for the Pegasus's 2-missile firing system).
• Now that you have reached the final round, this is where things get tricky. It has a Zoltan Shield which absorbs 12 points of damage AND regenerates when it doesn't take damage, so you will need to take it out before you can teleport in and take out the weapons. After the weapons have been taken care of you will need to take it out as quickly as possible; power down the teleporter and pour everything you have into the engines so that you can dodge the super attack. Alternatively, one can use a well-timed Level 1 cloak to dodge the super attack. This super attack shoots around eight Heavy Burst Lasers and is charged by the teleporter platform - this means that even if all of the weapons are offline you can still be hit by this. Take out it's shields as fast as possible then aim for the teleporter to delay the next super weapon shot.
• Congratulations! You have beaten the Rebel Flagship!

Boarding Strategy:

So far I've found this easiest with Mantis B, but I've also done it with Stealth A and B, Rock A, and Kestrel B.  (I don't have the Crystal ship yet).

Recommended equipment, system levels, and personel:

• 4 gold level boarders.  Mantis, Rock, and Crystal are the best so try to pick up these crewmembers whenever possible.
• Level 2 or 3 teleporter.The large one isn't required, but if yours is small you definately need it to be level 3 (or you need the healing bomb).
• Level 2 or 3 shields.  Level 3 is safer, but level 2 is manageble with a high-level engine and a defense drone mark 2.  Level 4 is just a waste of scrap.
• Level 6+ engines.  More is better.
• Level 1 cloak.  The super weapons the boss has fire off about every 25 seconds or so, so level 2 or level 3 cloak won't allow you to recloak in time.
• Defense Drone, preferably mark 2, though mark 1 also works well.  With 4 boarders I also really like the system repair drone.
• Breach bombs, Pegasus Missiles, or Breach missiles.
• Any sort of laser or beam weapon (the power of the weapon doesn't matter here, except to make fights shorter).
• Level 2 or 3 doors.
• Level 2 medbay.

Round 1:

• Start by turning your defenses up to maximum.  At the moment, you don't need any more offensive power than your teleporter, so turn your weapons off if it means having level 3 shields and near-maxed engines.  A defense drone is nice here, but isn't required yet.
• Teleport 2 of your boarders into the missile launcher room (just to the right of the cockpit).  Don't retreive them until they destroy the weapon.
• As soon as your teleporter is off cooldown, send your other boarders into the ion weapon room.
• When possible, retrieve your original boarders and then send them into the beam room.
• When those three weapons are dead, the only attack the boss has is the triple heavy laser.  If you have a level 3 shield, feel free to reroute power from your engines to your weapon systems.
• After your boarders have been healed in your medbay, use your missiles or bombs to destroy the boss' medbay.  (If you used breach weapons, wait until they fix the breach before continuing).
• Heal Burst is quite useful here.
• Get all of your boarders into their medbay as fast as possible.  You should be able to kill nearly all of their crew before being forced to retreat since they won't be able to heal themselves.  If you need to pull your boarders out, repeat the last two steps until only the gunner to the left of the cockpit is alive.
• Have your boarders take out the shield generator then pull them out.
• Use whatever weapons you like to destroy the helpless boss.  It is mildly amusing to destroy it with a weapon only poor transport ships use (the dual lasers).

Round 2:

• Switch back to your defensive setup, but make sure that you have a defense drone on.  You really don't want to have your non-combat crew having to deal with boarding drones here.
• Remember to use your cloak when you see the power surge warning.  The extra six drones are the scariest thing the boss has, but fortunately it lasts for only five seconds.
• Teleport 2 of your boarders into the missile room again and take it out.
• When your teleporter has recharged, send your other two boarders into the drone control room and destroy it.  This will stop the annoying boarding drones, the defense drone, and the normal anti-ship and beam drones the boss uses.  Turn off the defense drone, and use that power to activate your weapons.
• Once the missiles have been destroyed, have those two boaders switch to the beam weapon room.  Once that is destroyed, have them join the second group of boarders in the main section of the ship.
• Once the drone control is destroyed, take out the shields.  Then retrieve your boarding crew.
• Kill the boss again with whatever weapons you see fit.

Round 3:

• Switch back to defense mode.  Note that you do need at least 1 weapon active here.  Don't forget to activate your cloak to avoid the super weapon shots.  (Can also get you an acheivement in the stealth cruiser).
• Take out the Zoltan shield.
• Send 2 of your boarders to destroy the missiles (again).
• Send the other 2 to take out the teleporter, then the shields.  You may need to take out the Zoltan shield another time or two.
• Once the normal shields are down, retrieve your crew and destroy the boss (again) with your amazingly powerful dual lasers and/or leto missile launcher.

The hardest part is taking out the crew in round 1.  After that it's a pretty easy fight as long as you leave the near-useless heavy laser gunner alive.

Possible Strategies (Normal Difficulty)

• Not everything is going to be handed to you on a silver platter. You have to adapt to a lot of situations in order to win. You can beat the boss without maxed out weapons, but all other systems must be adequately upgraded, or you won't stand a chance. Evasion is just as important as shields and weapon control, just not in early game. Also, having a weapon that can bypass shields (I.E Missiles, bombs, Artillery Beam) will be incredibly useful, but not mandatory. It would be wise to have at least enough firepower (excluding weapons that bypass shields) to take out 4 shields AND hit a room at least once. Drones, especially the defense drone, will be incredibly helpful as well.
• During the first stage of the boss fight, your main priority are the weapons, since they cannot be repaired if you kill the crew manning them (unless you kill off all of the crew/ship teleports away). Go for the triple missile launcher first if you don't have any defense drones, otherwise take out the triple ion blast. If you're not doing damage fast enough, then it might be a good idea to focus fire their shields first. Low damage or shield penetration will prevent you from damaging the flagship's weapons fast enough to protect you. If you have missiles/bombs, use those to take out the shields, then use your lasers to take out the weapons.
• During the second stage, it loses cloaking and ion blast, but starts using drones. It also has a special move telegraphed by the "power surge detected", which releases many more laser and beam drones. Disabling the drone control will not nullify the power surge, but will deactivate any other drones, particularly useful when the flagship has a defense drone. The Flagship will also release boarding drones. They will harass your crew non-stop, since you can't "guide" them to your medbay by opening all the doors except some. However, after a large number of defense drones, the flagship will eventually stop launching them. A defense drone of your own can quickly cut through those reserves. You want to target either the triple missile launcher or the drone system.
• Finally, the third stage, and the easiest if you have good shields and evasion. The Flagship starts off with an enhanced Zoltan Shield, taking more hits than a regular super shield would. In addition, the power surge shoots  many lasers at once, OR fully recharges the super shield. It only has a triple heavy laser, and a triple missile launcher as weapons. This is a problem unless you have a weapon pre-ingniter because he can get a few shots off before you even take down the super shield, and possibly get a power surge off before you do any real damage. If you have 50% evasion and three layers of shields, the power surge should do little to no damage. The flagship will also start using it's teleporter. Thankfully, they can be "guided" to your medbay, and humans are only average in combat. Focus fire their shields or their weapons.
• Congratulations! If you have beaten the Flagship then give yourself a pat on the back, because Normal difficulty doesn't mess around. These tips are just guidelines, because situations will vary depending on the circumstances. Adaptability is key.