There is only one way to win the game and that is to defeat the Flagship at The Last Stand. Everything you do up until then must be focused on preparing your ship and crew to win that fight. Every upgrade you choose, every item you buy in the store, every point you jump to, every dialogue option you choose must be the one that improves your odds against the Flagship. Never buy 'nice' augments or make frivolous upgrades. Never buy more fuel than you need or repair more than necessary. Guard your hit points and conserve your drones.

All that matters is the Flagship.

Forgetting this commandment will cost you more games than any other.

You will lose the game from damage in more ways than just running out of hit points. Every point of damage you take will cost you scrap to repair, scrap that you would otherwise use on upgrades. Every system that is knocked out when fighting an enemy will cost you time in killing it. That time will be an opportunity to take more damage. Taking damage starts a cycle that accelerates; once you start getting damaged in a fight it is often hard to stop.

Bottom line: unless your ship has no shields or starts at Level 2, the first 50 scrap you spend must be on Level 2 shields. Follow this up with any reactor upgrades you need to make that more manageable. I have done the spreadsheets up and down, and no other upgrade in the game will spare you as much damage as Level 2 shields. It will make you immune to many of the ships you will encounter in sectors one and two. It will protect you well in sectors three and four. Upgrades to your engine are cheaper and they improve your evasion which will counter missiles and bombs. But don't be tempted. Evasion becomes more effective at mitigating damage when the enemy is firing many shots. In the early game, you will not see many ships with a high burst. Shield 2 will mitigate more damage against an average ship in the first four sectors than any other upgrade.

If you do happen to be in a ship with no shields, your first priority at a store is always to purchase shields. You may need to make ship upgrades beforehand (upgrading your cloak in Stealth B or upgrading your drone control in Stealth C) to make your ship more survivable, but keep your eyes on the prize: buying shields.

After upgrading to Level 2 shields your priority should be finding a Defense Drone 1. The DD1 is such a key upgrade that it gets its own commandment as it does more than just mitigate damage. If you have excess scrap, continue to upgrade your shields to Level 3 for 150 scrap and then start improving your engines. Only if your ship has Level 1 engines should you consider upgrading them early.

The Defense Drone 1 (DD1) is the single best purchase in the game. It will cost you 85 scrap and will defend you from missiles, drones and hacking attempts. The DD1 is superior to its more advanced brother, the DD2 because it will only target hard ordnance. The DD2 will often shoot down a laser blast your shield would deflect and ignore a missile or drone fired at the same time.

Missiles are the single biggest damage dealer that you cannot defeat just by upgrading your ship. If you do not evade them, you will take damage and damage is bad (see Commandment 2). Worse yet, missiles do extra crew damage, set fires and have a better breach chance than other weapons. Fires and breaches will delay system repairs, so a missile hit to a critical system can cripple your entire ship.

A DD1 will defeat about 90% of all incoming missiles, effectively eliminating the biggest HP threat in the game.

Let me repeat that:

A DD1 will defeat about 90% of all incoming missiles, effectively eliminating the biggest HP threat in the game.

It gets better too, if that were possible. DD1s will shoot down boarding drones and ion drones. Either of these two drones will create a breach where they hit making them tough to kill. Ion drones will stun all your crew when they fire and boarding drones will rapidly destroy systems if unchecked. Dealing with a boarding drone causes the type of ship disruption that will cost you hit points. DD1s will also shoot down enemy hacking modules. Getting hacked can be crippling if the drone hits a vital system. They will strip shields, drop your evasion to zero, uncharge your weapons, kill a hapless crew member in the Medical Bay or even suffocate your crew. The only reliable hard counter to hacking drones is the DD1. Just like a boarding drone, a hacking module does no damage itself, but the disruption it causes will lead to damage you must avoid.

The Flagship will use Hacking on you in the first phase and Mind Control (MC) in the third phase. Both of these attacks are extremely dangerous and can cause the demise of an otherwise well-equipped ship. If you want to take down the Flagship smoothly, you will need to fight fire with fire. Having Hacking and/or MC will greatly improve your odds against the Flagship. Remember the First Commandment. Even if you never use MC or Hacking against a ship prior to the Flagship encounter, you will need it for that fight.

There is only one obvious system to hack on the Flagship and that is the shields. A Level 3 hacking module will leave the Flagship completely without shields when it is at full effect. That alone changes the Flagship fight from hard to pitifully easy. As an extra benefit, the door lockdown from hacking the shield room on the Flagship prevents enemy crew from moving too and from the laser and missile launcher rooms. Enemy crew will be unable to quickly repair those weapons if the shield room is hacked. Hacking can be used on Stage 1 as soon as the Flagship decloaks. It can be used on Stage 3 as soon as the Super Shield is down. A single DD1 on Stage 2 will prevent you from hacking, however. A Defense Scrambler will allow you to hack on Stage 2 and if the DD1 is knocked out for any reason, you can quickly launch a hacking module. But the upside of having a cakewalk in Phase 1 and Phase 3 is that you can slug it out in Phase 2.

Mind Control is also devastating against the Flagship. If you have poor firepower, MC the pilot to drop the evasion down and start scoring hits on the shield room. If there are four enemies repairing damage in the shield room, MC one of them to stop them from repairing. Then let loose on the shield room to kill off the crew while the fight. MC the missile launcher room to delay or knock out the launcher. MC combined with a hacked shield room will allow you to cripple the Flagship quickly. It is not even necessary to upgrade MC to have great results. You want to disrupt the enemy crew, even if your MC'ed target isn't buffed to level 3. But beyond all these great benefits of MC, having MC will make Stage 3 much easier. The Flagship has Level 3 MC on Stage 3 and will rapidly board your ship with its crew. The ONLY hard counter to enemy MC is your own MC. As soon as one of your crew is hit by the Flagship MC, use your own to flip him or her back. Neutralizing Stage 3 MC will allow you to keep your stations manned throughout the fight, deal with the boarders and finish off the Flagship in short order.

The crew bonuses for training are important and significant. The evasion bonuses from pilots and engineers and the firing bonus of gunners are especially important. Make sure your crew is put in the best positions. Zoltans are best in the shield room, where their unstrippable energy will protect you against ion weapons. Rocks should be placed in central compartments to compensate for their poor speed. Humans make great pilots, gunners and engineers as they quickly gain experience. If possible, keep your Engis and Mantises out of trained positions. You want your Engis to be free to quickly move to damaged or burning compartments. You want your Mantises free to deal with intruders.

If you have followed Commandments 2 and 3 you will often find ships, especially in sectors one and two that cannot damage your ship at all. These ships are training ships and you should take advantage of the stalemate to allow your crew members to train their skills. Get up, walk the dog, make a snack, go to the bathroom, whatever. Waiting a few minutes will allow your crew to level up their shield and evasion skills. If you have a weapon you can fire back without damaging the enemy, set that up to autofire and rank up your gunner. It is hard to be patient here, but remember that a fully trained evasion crew will get you +10 evasion. That's two engine upgrades for free. A fully trained gunner drops the Glaive Beam firing time from 25 seconds to 20.

Keep track of your repair team and your security team. If you have a Mantis to guard against boarders, make sure that he or she gets the kills. If there are other crew in the room during the fight, have them leave right before the end so your Mantis can get credit for all the kills. If you have an Engi dedicated to repairs, make sure it gets credit for the repairs in the same way.

There are many different weapons and combos in FTL, but the only attacks that matter will be the ones that can defeat the Flagship. The Flagship has four shields and decent evasion. You need to take those shields down and then do damage. In order to do that you will need to fire a burst of at least 5 shots in the span of one second. This alone will not hurt the Flagship, of course. The weapons that follow up the burst are going to do your damage. The burst of five is simply to take down the shields.

Your follow up weapons should be your heavy hitters. Hull lasers, heavy lasers and beam weapons are preferable, but regular lasers are fine as well. If you have a Glaive Beam, you may be able to get away with a burst of three or four, but I wouldn't recommend it.

Some weapons don't fit into the burst category. Ion weapons are the first major exception. Ion weapons are primarily useful for their chaining effect to eliminate enemy shields. Although ion chaining is effective against Stage 2 and Stage 3 of the Flagship battle, it will not work in Stage 1 because of the cloak. Therefore, in following of the First Commandment, you should drop ion chaining by the time you hit the Flagship or have a secondary weapon layout for Stage 1.

Chain lasers will fire too quickly to be used in a burst when fully spun up. The Chain Vulcan is still a good weapon because it fires fast enough to chain down the shields even in Phase 1. The simple chain laser, though, should not be seen as anything more than a Burst Laser Ir that fires slowly to start. The advantage of the simple chain laser, the 7 second firing rate cap, is worthless as you will need to time it to fire with slower weapons. Therefore it is both more expensive and less useful than a Burst Laser I. It should be avoided if possible.

Burst Laser III, although firing five shots in a single volley does not fire quickly enough for it to be considered a five shot burst. It is difficult to connect with a heavy hitting weapon after the five shots because the Flagship shield may already recharge. This is especially problematic if your heavy hitter is a beam weapon.

Missiles and bombs are all-or-nothing weapons that are unreliable in the end. Defeating the Flagship will require a reliable weapon setup, therefore you should avoid builds that require missile and bomb hits. This is probably the most controversial of the tips so I want to stress I'm not saying "Don't use bombs and missiles." Just don't rely on them. If you have a solid ship, there's no harm in adding more firepower.

The downside of missiles and bombs is not just limited to their hit or miss nature. Missiles can be easily neutralized by defense drones, which are used by many enemy ships including the Stage 2 Flagship. Both can also be neutralized by Zoltan Shields. Missiles and bombs tend to have a slower firing rate than laser weapons. This is especially true for bombs, which are some of the slowest firing weapons in the game. Time spent in combat is time you could be taking damage. Finally they cost ammunition. When the only thing keeping you alive is the profligate use of all your available weapons, you never want to be in a situation where you're deciding whether to fire a precious round or take a few hits.

Attack drones suffer as badly as missiles in the final analysis. Although they attack quickly, they are arbitrary and cannot be used well in a burst. They cost a significant amount of energy to use and can be neutralized by Anti-Drone Drones. And, like missiles, they cost drones. Drones are precious because you will want to be using your own Defense Drones (Third Commandment).

One of the simplest, but most easily forgotten Commandments. It is also one that will kill you all too frequently. Being caught by the Rebel Fleet in Advance Hard is almost always fatal in the early sectors. Even if you escape, you'll have taken a ton of damage from the Rebel ABS. In later sectors, upgraded engines or stealth may allow you to avoid the ABS and jump away safely. But the Elite Fighters are always tough customers and you get no reward for defeating them.

Each Sector Map may have dead ends and points that look like they connect but do not. Every time you jump into a new sector, spend a few seconds to plot a reasonable path through it and make note of traps. Ten seconds spent at the beginning of each sector will likely spare you some embarrassing trips back to the hangar.

All crew members are good, but Zoltans are in a class by themselves. Their special ability of providing one un-ionizable energy to their room is amazing. A reactor upgrade costs 20-35 scrap itself. A Zoltan may cost 60, but you get crew and a free reactor upgrade. You can never have too many Zoltans.

A pair of Zoltans in your shield room will always give you one layer of shields that cannot be stripped by ion weaponry. Four will make you practically invulnerable to ion weapons. Zoltan crew will allow you to exceed the normal limits for your ship performance, allowing you to run more shields, engines and weapons. Zoltans are awesome.

The simplest of the Commandments. Upgrade your piloting to Level 2 or Level 3 before confronting the Flagship. A single hit to a Level 1 bridge will drop your evade to zero and force your pilot to begin repairs. Against Flagship events like the Stage 2 drone swarm or Stage 3 super weapon, a 0% evade will devastate your ship.

Upgrading piloting is cheap, easy, and will save your ship.

Seriously. Giant alien spiders are no joke!