Ship Strategies

This page contains community strategies for various ships in FTL; your mileage may vary.

Kestrel Cruiser

Layout A

Starting weapons are some of the best in the game, and players will likely keep one for the whole game. The Artemis is excellent for midgame, when just your 3 lasers aren't cutting it, while the Burst Laser II destroys in the early game when unopposed, and in late game if you can find it some support. Adding beam weapons is an excellent idea, due to this ship's high shield removal capabilities.

Layout B

The Basic Laser doesn't pack much of a punch individually, but four of them become very effective for early and even mid game. The crewmember manning the weapons will level up very quickly. Over the course of the game, you should slowly replace the Basic Lasers with either support (bombs, missiles, beams) or stronger lasers to create truly frightening salvos.

Layout C

The ion stunner prevents people from repairing the system they're in, if combined with the hacking + the augment hacking stun, they'll be unable to repair their shield, and you can focus down their weapons. It's also amazing in combination with a weapon that creates fire or hull breaches, since they won't be able to or go to the health bay or douse the fire. A teleporter is also nice for your Lanius, just be sure not to stun him while he's in the room you're ionizing. It's layout is amazing for dealing with boarders just have someone sitting in the weapons room, and it should be smooth sailing. Send in your Lanius if you need to distract your boarder or drain the oxygen faster, be sure to temporarily turn the off the oxygen system to speed this up. If you've got an important fight coming up, and you've got a party with low health, kill them and get them cloned, so they won't get killed at an inopportune time.

Stealth Cruiser

Layout A

This ship poses an unusual challenge as it starts without Shields, but if you compensate by correct use of your built-in cloak, you will be fine. Cloak as soon as the battle begins to give your weapons time to charge - the enemy weapons won't be charging while you're cloaked. From your starting weapons, use the Dual Lasers to take away the enemy's shields then use the Mini Beam to do some damage. By aiming both at the enemy ship's weapons, you'll usually prevent any return fire. Upgrading your cloak should be your immediate priority, followed by acquiring an additional shield-downing weapon, followed by acquiring an actual shield module (which is sold in some stores for 125 scrap). If you make it through the first couple sectors in one piece, you'll find yourself in great shape.

Layout B

If you're a risk-taker at heart, the Layout B Stealth Cruiser can be a great ship for taking on the higher difficulty levels: you may die a few times in Sector 1 or 2 getting started, but if you make it past the beginning you'll be in superb shape. That's because you start with not only a Cloak but one of the best weapons in the game, the Glaive Beam. You'll be a bit vulnerable during the 25 seconds it takes to charge, and its 4 power requirement means that any hit to your weapons will interrupt the charge and likely leave you trying to beat a hasty retreat, but net of enemy shields the Glaive Beam can do 9-15 damage (3 damage per room × 3-5 rooms) in a single shot (depending on the enemy ship layout) and has a chance of lighting enemy rooms ablaze. Early on, you’ll need to rely on your cloak to avoid damage: depending on the tactical situation you have the choice to cloak immediately at the beginning of battle to keep the enemy weapons from charging and delay boarders, or to cloak when the enemy ship launches its first volley, usually causing it to miss and be wasted thus gaining even more time. If you can buy enough time for your Glaive Beam to fire you usually won't take any damage after that. In the first couple sectors, you should be able to kill most ships with one shot, so your goal should be to avoid as much damage as possible until you get your shot off. For ships that have shield strength one, start your beam in their shield room: the subsequent rooms will take full damage. Your Cloak starts at level 2 and should be upgraded to level 3 as soon as possible, giving you longer to get your Glaive Beam charged without taking damage. Once you get through the first couple sectors, focus on finding new ways to take down enemy shields; the Glaive Beam will do the rest. Once you're out of survival mode, try to build up a reserve of 125 Scrap so that you can pick up Shields at a store. Note that the engines only have 2 bars. Hacking is also a valuable asset, as it can easily drain up to 4 layers of shield, leaving the enemy shield defenseless against the power of the Glaive beam. 

Layout C

The vulnerability of this Layout belies its potential strength. Unique to Layout C is a more power efficient version of the Shield Overcharger, and it's also the only non-engi ship to possess a 3 space drone bay, giving greater versatility for Drones to be used, either defensively or offensively. Indeed, combining this specialised Shield Overcharger with 2 Defense Drones Mark II (for a total of 8 power - the max) could render a normal shield system useless - granting near-invulnerability to hacking, (non event) boarding, and a large number of projectiles, provided your drones are up as soon as battle starts and enemy weapon systems are targeted first.

Furthermore, a slightly improved version of the Laser Charger (S) gives versatility in early combat - important with only 3 weapons spaces. This hints at the strength of charger weapons in general. Storing multiple charges allows for a focused fire to punch through defence, at which point single charge shots can be used to chip away at the enemies systems (shoot weapons first).

This all comes at the cost of the Cloak however, meaning the early game is significantly harder until suitable defences are acquired and upgraded.

This Layout does still keep its Long-Range Scanners - and these will be vital early on to avoid dangerous environments, of which asteroid fields are by far the most deadly. However, once you've obtained suitable defences to the main dangers FTL has to offer it might be wise to trade this augment in for something more useful in direct combat.

It's highly suggested to install the Cloaking system, as this will add synergy to generating layers of the super shield and building up weapon charges, and give some further defence against Ion weapons, leaving just beam weapons and drones as threats, which can be mitigated by either a hacking device or a skilled boarding team.

As this build is so drone-heavy, acquire a Drone Recovery Arm - and your defences become free! It can easily be swapped out towards the end of the game (Sector 6+) when you should have stockpiled a large number of drones.

Mantis Cruiser

Layout A

The Mantis Cruiser is one of the few ships that have no starting Sensors on board, which makes getting information of your ship status difficult. It is possible to buy a Sensor system if you find one in a store.

With 3 mantis, an engi, and a teleporter, it is hard to mess up in the beginning, annihilating enemy crew. However, because of tiresome balance, it has no sensor, the starting weapons are weak, and you can only have one activated at a time. When facing AI ships, use the Small Bomb on the shields, then peck at it with the basic laser. With zoltan ships, take down the shield with the basic laser, then proceed as normal i.e. killing the enemy crew.

Later on, you'll need stronger weapons, but that isn't too hard with your increased scrap gains. Go for peaceful areas for easier pickings, then upgrade your weapons until teleporting and weapons work together. Alternatively, get drones and boarding drones to completely dominate boarding.

Layout B

With 2 shields, it's unlikely that many enemies early on will be much trouble, but the piloting and engines only have one bar. Focus on getting level 2 piloting and engines A.S.A.P. to have any dodge chance. If the enemy has missiles, use the defense drone if you send your entire crew over. However, you don't need to worry about your crew being stranded, as if the teleporter is damaged and there's nobody there to repair it you'll get an event about taking a shuttle back to your ship. For AI and zoltan-shielded encounters, just pop a defense drone if needed, or use a zoltan shield bypass augment to get past the shield in advanced edition. and wait until you can jump away (or get level 2 teleporters to chip away at systems). Taking them on with boarding drones is impractical and not worth it early on, unless it is the AI variant with doors linking the 5 rooms. Focus on getting crew and weapons as early as possible, so that AI and manned ships are nothing to you. This ship is extremely powerful later in the game if you chose to board frequently. Just be careful not to lose 4 crew members to a fleeing ship or forgetting to turn off your cannons.

Layout C

This ship has trouble earlier on in the game (especially with A.I. Ships). Having no damaging weapons can be a problem. However, you have a lanius, crew teleporter AND a stun bomb. You can teleport a lanius and some mantis over to a four-room system, wait for your stun bomb to charge and get your mantis out of there and stun the heck out of the room the lanius is in. Nothing will be able to attack it, and the oxygen will slowly get drained away in that room, killing off the possibly 4 enemy crew members in there while your mantis wrecks other systems. It is recommended to get some sort of weapon that can actually deal hull damage, so that you don't have to jump from every A.I. Although, if you send a lanius to the weapons system, you can disable the offensive capabilities, and every time you break the weapons, it deals 1 damage. If you are patient, you can destroy an A.I. ship by destroying the weapons every time the drone repairs them- the cloning bay will recover the lost lanius. Ship and have big problems with Zoltan Shields. zoltan Shield Bypass and Reconstructive Teleport are good augments to have, especially Reconstructive Teleport with a clone bay.

Engi Cruiser

Layout A

With shields and a non-lethal weapon, if you happen to find yourself up against a non-threatening (carrying only a non-piercing beam weapon, or one single-shot laser), non-retreating target in the early game, you can easily train your crew member's skills, if you're so inclined.

Set your Ion Blast Mark II to autofire into the enemy ship, position your crew members in the room you'd like them to gain skill in, and walk away. This is suitable for almost all ships that can't pierce your shields, and if you get bored, fire Ion on enemy oxygen to have extra fun and benefits.

It is possible to completely level all your crew members in all disciplines but repairing (weapons, shields, engine, and piloting) this way. The bonuses that high skill levels offer are huge and potentionally gamebreaking benefits.

A key addition to this ship are bomb-type weapons. Ion Bombs are great later in the game against enemies with more than 2 shields, including the Rebel Flagship. The Ion blast and bombs can keep the shields down while your drones go to work on the hull. A Small Bomb or other type of launcher can selectively take out systems as needed. A Drone Recovery Arm is great, too, because it allows you to use your drones unfettered. Upgrade doors because Engi are weak at hand-to-hand combat, and if you have the opportunity to get Rock or Mantis crew, do so. The Teleporter is not advised on this ship, unless you are getting the system for blue storyline options.

It's worth noting how ridiculously powerful multiple attack drones can be. Early on, two attack drones will bring down shields and slaughter ship hull, while later, upgrading one attack drone to Mark II or getting three can take down even 4 layer shields. Add your own weapons and the enemy will start crying.

Layout B

The initial armaments are decent and cover all angles in the beginning, but the ship gets hard to use quickly. The layout of the ship is one of its advantages, it's tightly packed so it's easy to reach any point of the ship, and that can make it easily manned later on, the teleporter and medbay are next to each other so you can make this a decent boarding ship, though as only the airlocks are empty rooms any hit that gets through the shields will most likely hit something important. The starting crew is mostly stuck at the helm, you have to use your drones to repair systems, and to fend off boarders, and your starting weapons are barely enough to get you by the first 2 sectors. It's a good idea to have most of the ship vented, and investing in lvl2 blast doors to lock the boarders in the vented areas (only the helm and medbay and the room in between need oxygen) until you get more crew, and as soon as you start to get more crew, it's wise to swap most of the on board drones out to more offensive ones (and thus rendering the initial augment of the ship mostly useless so you may as well sell it), unless you get really lucky weapon drops/shops early on, as it's easy to fill the maximum of 8 power sockets with 3 powerful/decent weapons. If you can't get crew, better weapons, or offensive drones fast enough (the more of these the better) you'll have a really hard time beyond sector 2 where you cannot find opponents with less than 2 points of shields. In the end this ship has a rough start so if you want some extra challenge from the game, fly this ship for fun.

Layout C

Starting with a Defense Scrambler and a Beam Drone, this ship depends on removing the enemy shields via hacking and the Dual Lasers. Drone parts are often a major concern, and you are unable to shoot through level 2 shields without using some. Upgrading hacking early-on helps you keep down the enemy ships' shields much longer, so your beam drone can wreak havoc and damage the enemy ship.

As the door subsystem is located next to the piloting seat, you needn't upgrade doors as much as you have to with the Layout A or B. Therefore, you may spend your early scrap on getting another layer of shields, and some bonus evasion. Getting some more offensive drones is also recommended, as the synergize very well with the hacking. A drone Recovery Arm is particularry useful early-on

Later, this ship usually relies on its hacking and massive drone army to destroy the enemy ship. Due to the Defense Scrambler, Anti-Combat drones should not be a problem, and the drones destroy Zoltan shields pretty easily. However, without upgrading weapons, this ship cannot take out specific systems/subsystems, so having Mind Control, Teleportation and/or some advanced weaponary is highly advised against the Rebel Flagship.

Federation Cruiser

Layout A

The Artillery Beam ignores shields and does a lot of damage, so it is a good idea to strengthen the defenses (shields/engines) and let it do the work. This needs patience, but is worth the wait. If possible, destroy the enemy's missiles promptly (or get defense drones), as they bypass shields and hence pose a threat to the hull.

The Artillery Beam's path follows a specific algorithm. It finds the centers of two rooms and forms a path between them, with no limit on the length between them.

Layout B

Layout B also features the Artillery Beam, but starting at level two right away. As with Layout A, strengthening the defenses stays a priority. One might also find that the room layout is quite ideal to fight off boarding parties by opening airlocks.

The basic two shot laser you are getting with this layout however also punches through early one level shields, which gives a comfortable start through the first sector. It's also easy to expand this setup, since more lasers add up nicely with the first one and a teleporter combines well with the overall defensive approach. As soon as you have a teleporter, you can punch out single systems like the medbay with lasers to support your boarding, rather then leveling everything with the Artillery Beam.

Just be aware that the first missile launcher mostly wastes missiles and should be seen as a last resort for the first sectors.

Also for both layouts it should be noted, that since the Federation Cruiser does not get a cloaking device (excluding Advanced Edition), two defensive drones mark I or one drone mark II are a grand choice for the final battle. Attack drones - just like beam weapons - don't quite combine well with the ship, however

Layout C

Layout C is, for the most part, a boarding ship. It has an Artillery Flak Gun instead of an Artillery Beam, which can be used to shred a Zoltan supershield, for instance, before beaming in on your teleporter.

Due to the Clone Bay installed and the addition of Zoltans exploding upon death, this ship requires you to suicide bomb the opponent. As a result, a Level 3 Cloning Bay and a Level 3 teleporter go well together. Zoltan ships are not as much of an issue as they are to other ships, since the Flak Gun with punch straight through them, and you can suicide bomb Drones to submission.

Note however, that the Artillery Flak Gun lacks the shield-piercing capacities of the Artillery beam, meaning that it's essentially a slower-cooldown or more power-hungry version of the Flak Gun II. It still has its uses, however, as investing just 1 power can result in a punch-through burst later in a fight when combined with your other weapons, but unlike Layouts A and B it's simply not viable to rely purely on Artillery.

An alternative option is to level up the weapons system and rely on beam weapons and the Flak Artillery later on (the Flak Artillery, when fully powered on it's maximum rank has the same cooldown time as a Expert-manned Glaive Beam). This way, you can remove enemy shields with the Flak, and immediately follow up with up to 4 different beam weapons, leading to devastatingly high damage.

Slug Cruiser

Layout A

You begin with the Anti-Bio Beam, which usually takes 2 hits to kill an enemy crew member, 3 if the enemy crew member is a Rockman or Crystal since the weapon does 4 personnel damage (1 personnel = 15 hp). Later on, if you can deal some damage with normal weapons or boarders, you can reduce Rockman, Crystal and Zoltan hits by 1 fairly easily.

There are no sensors aboard this ship. However, Slugs can see the rooms they are adjacent to, and the locations of enemies onboard their vessel.

The weapon systems equipped on the default Slug Cruiser are designed to kill enemy ship crews. The Breach Bomb (which uses a missile) does good personnel damage and damages systems but does no hull damage. The Anti-Bio Beam does heavy damage to crew but none to hull or shields. The Dual Laser (with its two shots) should be used to temporarily disable shields, with the Anti-Bio Beam being fired immediately afterwards. This will allow the Anti-Bio Beam to bypass shields without having to destroy the enemy Shield room first. If both Dual Laser shots hit, you can successfully engage ships with two shields with the default weapon loadout. Ion weapons can be a good supplement to the Slug's arsenal. Caution is advised, however - this strategy doesn't aim at either the helm (to reduce their mobility) or weapons (to reduce their offensive power). Patience and a decent shield will be your best weapon with this strategy.

Try to stick to slug only members, so you have 100% immunity against mind control. Viable systems are hacking for taking down shields, mind control for weakening enemy crew, and teleporters if you're other weapons aren't cutting it.

As for the flagship: board the missiles, hack the shields, mind control the pilot, to nullify their dodge chance, and the crew members can't do anything about it, since hacking disables their doors, thus it'll take time for them to get another pilot. Be sure to also take down their shields with something like a breach bomb, which will their ship rendered useless ,(this also works for difficult mode, so you'll slow them from repairing the missiles/lasers)

Layout B

Initially lacking both a medbay and sensors, plus only missile-utilizing weaponry, this ship can be very difficult to manage, and is more a challenge for the experienced than a realistically balanced beginning ship. The focus early-on should be on conserving missiles and scrap, for otherwise you'll end up expending both very quickly. Fortunately, the starting teleporter can give you an edge, especially when used in conjunction with the Healing Burst, if used with precision. Artemis missiles should only be expended if the enemy ship's weapons are particularly threatening, or if they have a medbay.

If you play your cards right and frequent stores, the securing of ammo-less weaponry and your own medbay system ensures a much smoother ride. As a slug ship, you need no longer fear nebula systems, and by aiming for them, you earn yourself bonus time to explore, thus earning more scrap with which to upgrade in preparation for the endgame. Also, with five airlocks and pre-upgraded blast doors, ship defense, most common in nebulas, is a breeze.

Layout C

One of the most versatile starting ships and the only ship to start with both Mind Control and Hacking, this ship has many different and powerful builds, especially with a starting Chain Burst Laser. Early-on you can easily make enemy crew suffocate by hacking then destroying the enemy ships' Oxygen system, and then Mind Controlling the enemy crew trying to repair it. Should they still be able to repair it, you can reactivate hacking to drain it further more, and destroy it with another volley of your starting Laser. This way, you can have increased rewards in the early sectors, which can give you an edge later if you invest in more shield layers, increased evasion and/or more powerful weapons.

Starting with a level 2 Doors subsystem and a Mind Control, this ship is quite strong against early boarding parties. Be careful, though, as Mind-controlled enemies can pass through your doors just as if they were friends!

Later, this ship can be enhanced a couple of ways. Due to hacking, both Drones and Beam Weapons are a great addition to its arsenal, as Hacking can remove enemy shields. Alternatively, you can acquire weapons cabable of firing many shots, and disable the enemies' helm or engines, leading to a guaranteed hit on all your shots. Bombs synergize very well with your Oxygen-denying capabilities, and Teleporting is also a welcome addition, as you have Mind Control to turn the battles' tides, and Hacking, which can serve as a weaker Lockdown.

Rock Cruiser

Layout A

With the two missile launchers you start out with, you can easily penetrate shields, removing the difficulty of having to disable shields before damaging systems. Try to conserve the missiles as much as you can; 28 might seem like a lot to start out with, but it goes fast when you fight tough enemies. If the enemy ship has four hull left, instead of using two artemis missiles, conserve by using one hull missile instead; in fact, it may even be worthwhile, especially if they have slow repairman, to first knock out enemies' weapons with the artemis, then maximize damage by only targeting empty rooms with hull missiles for the remainder of the fight. All of the doors and empty rooms allow for you to suffocate enemies easily. The rockets make fighting ships with Defense Drones hard, but firing both at once forces the drone to shoot only one. The rock plating allows you to worry less about shields up until around sector 3 or 4, when the enemies start leveling up their shields.

Layout B

The pierce laser makes this ship more than a match for most early enemies you encounter. There are many ways to play this ship, but making use of the fire bombs is especially fun. They are ridiculously powerful when used correctly. To do this, you'll need a teleporter ASAP. Once you have the teleporter, firebomb a high-priority room, and once the charge goes off, teleport 2 rock crewmembers into the burning room. If your enemies aren't rock people, they will take damage from the fire while you fight them, as well as the system in the room. Systems cannot be repaired if they are on fire, and fires cannot be put out if your crew is there. When you start encountering ships with med bays, these will be top priority. Enemies exhibit very strange behaviors sometimes when their ship is on fire. As a result, the achievement for killing a burning enemy crew member can be extremely difficult to get, although the crystal lockdown ability makes this easier.

Conserving a hull breach in a systemless room may prove useful as it can be used to vent rooms. Use with caution!

Layout C

The Heavy Crystal and the Swarm missiles can make early sectors quite easy, as you can penetrate a layer of shields without any problem, therefore you can focus your funds on defence early-on. Selling the starting augment is a great option, especially on higher difficulty levels, as you have drastically reduced scrap rewards there.

This ship's greatest advanatage is its Crystal crewmember, who can make defending against boarders much easier, and can be a valuable asset should you invest into boarding. It is also much easier to unlock the Crystal Cruiser with this ship, as you needn't get the pod and find a Zoltan Research station to get a Crastalline Being.

Later, you should replace your rockets eith some non-missile weapons, and get some stronger armaments to be able to destroy the enemies, or invest in boarding, either with a Mantis or Rockman and your Crystal crewmember. Crystaline Beings are also great when paired with Lanius, as they can lock enemies into Oxygenless rooms, while themselves suffer only reduced suffocation damage.

Zoltan Cruiser

Layout A

Proper use of the Halberd Beam makes the first two sectors of the game fairly straightforward, because most enemies will have only one shield level. Just remember to try to strike as many rooms as possible: begin at the tip of one room and cut corners of as many other rooms as possible. If you strike the enemy shield room, and knock out their shield, damage to any further rooms is doubled. For this reason, it is best to begin your beam sweep in a shield room, all other things being equal. Sometimes it is better to maximize the number of rooms you sweep, even if you end up hitting empty rooms; at other times it is better to take out key systems.

Once you start encountering enemies with two or more shield levels, you may want to use missiles to take out their shields or use an ion weapon. It is best to time your beam shots precisely when the enemy shield is hit, rather than putting your beam weapon on auto-fire.

Also note that the Zoltan Shield does not require the normal shield to be powered. So, while it is, feel free to take all your power out of your shields. If you improve engines, you can put the power saved from shields into the engine, which means you'll take fewer hits to that shield. As a general rule, when faced with a choice of buying a system upgrade versus extra power in the main reactor, it is usually a good idea to upgrade a system even if it cannot be powered continuously. This gives you more room to juggle power distribution and meet particular demands.

Other strategic points: The Weapons Pre-Igniter is incredibly valuable, especially for weapons with a long loading time like the Halberd Beam. Once you get a fourth crew member, move him or her into the pilot's chair so your former pilot's Zoltan energy can power one of the systems. (It's wasted in the captain's chair.) As with other ships, for the final battle it is advisable to have level 3 Shields, a Defense Drone Mk II, and a minimum evasion of 45%.

Layout B

With no shields, this is one of the most time-dependent ships that exists. Until you get 100 scrap for Level 2 Shields, you have to fight as fast as you can. Ionize shields and weapons (if you have Level 2 or better Shields and you are fighting a two-shield ship, just shields) to unleash the full potential of the Pike Beam.

Layout C

4 zoltans, a rank 2 Backup Battery and clone bay should fulfil all your zoltan-related needs late into the game. Your initial combo will be utilising the Ion Charger to disable shields while your drone demolishes the opponents ship, likely powering the drone with the backup battery.

Indeed, so reactor un-intensive is this ship that Ion storms, weapons and pulsar planets will pose little to no problem to you early on, giving a tactical edge against enemies.

You shouldn't waste power allocated to the shield initially, as it won't be hit until after the Super-shield is taken down, instead allocate to engines to preserve the Super-Shield longer.

Crystal Cruiser

Layout A

This cruiser starts with crystal weapons that ignore 1 shield and pass right through it. This is your biggest advantage, and it will be for most of the time since you don't need to take down the last shield, this makes fighting the flagship a lot easier, but don't get yourself in the feeling in the first few sectors that it will be easy. Most people spend their money on useless things and can't fight ships in sector 6 and above. It is very important that you buy more advanced weapons in sector 4, or at least get more low fire-power weapons. The crew teleporter is also a good choice since you get 2 crystal crew members with lockdown powers. If you manage to get a missile weapon and a laser (at least dual), this should be easy. For crew (that stay on the ship) you should probably use humans as they are the most multi-functional. Drone control is completely unnecessary if you have extra crew to fix breaches and put out fires. Cloaking might come in handy, but this ship doesn't lack evasion. Also when fighting the rebel flagship, if you lose the shields the Vengeance ability can save your life. 

NOTE: This is a very strong ship with many strategies, but is only advised for experienced players, due to hard unlocking and bad room arrangement.

Layout B

The only thing you can do is board enemy ships at the start, and this strategy continues to be the ship's best throughout the game. However, at the start, you can't get past Zoltan shields and AI ships are almost unbeatable without sacrificing a crewmember (The Crystal racial ability of reduced suffocation damage allows your crew time to damage and destroy systems without life support even with level 1 teleporters. The final, killing point of damage must be done with the Crystal Vengeance.) To do boarding without taking damage, you have to be fast. Beam 2 of your crew into the enemies' weapons room and lock it down with your Crystal Being power before the enemy crew enters the room. To get more time, use your stealth as soon as the enemy ship fires its weapons. You should be able to take down their weapon systems without taking any damage and beam in your third crew member to combat the enemy crew. The Crystal B is probably the easiest ship to board The Rebel Flagship with since there are three Crystal crew to lockdown the med-bay with and that gives you time to smash the med-bay, or pick off the crew one by one as they can't flee there.

With the addition of Advanced Mode, this ships position as one in of the best in the game is further solidified. At the expense of 50 scrap (or 10 if you sell the vengeance) a clone bay can be purchased, which eliminates the majority of weaknesses the original had.

AI ships can now be defeated by allowing one or more crystal crewmembers to land a killing blow - killing the crewmember but allowing them to be revived by the clone bay.

Any form of weapon to strip away Zoltan shields, or a zoltan shield bypass augment, and potentially a reconstructive teleporter augment (to heal the crystals without needing to resurrect them) and this ship can tackle any problem with minor expense. The only problem is it will take time, as damage can only be inflicted to systems by crew, and this does minor hull damage. Any weapon once the crystals have stripped the shields will expedite this.

Lanius Cruiser

Layout A

Layout B

Equipped with a Teleporter and Mindcontrol, this ship makes an excellent boarding ship. It also starts out with an adv. Flak, which functions similar to the Flak I. it fires 3 projectiles and can be used to great effect in the early to mid sectors. Usually, you'll want to target their weapons with the Flak and send your crew (2 Lanius, 1 engi to man the helm) to either the shields or the helm and mindcontrol one of their crew. The Lanius ability to drain oxygen together with mindcontrol is an effective way of taking out enemy crew. Since you start with a Clone bay, consider letting your boarding crew die on the ship to revive them with full health later. Alternatively, You can switch to a medbay or get the reconstructive Teleportation augmentation to heal your boarders. Focus on getting 2 Shield Layers early and hire additional crew members to man your other systems. Picking up a cloaking device is also a good Idea. You don't need a lot of weapons to effectively use this ship but to beat the Rebel Flagship you either need bombs and missiles to disable their medbay or enough lasers to pierce their shields and attack the medbay once the medbay is down, and all the crew (except the one manning the laser) is dead Its easy going from there.