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1''Send the crew to help immediately! YMMV tropes are no joke.''
2----
3* AssPull: One of the issues with the supershield / Zoltan Shield in ''FTL'' vanilla is that boarding parties can teleport into your ship as part of random events, and the game couldn't think of a good explanation for how [[LampshadeHanging the boarders managed to get past your Zoltan Energy Shield]]. ''Advanced Edition'' finally gives an explanation: the Zoltan Shield Bypass. Sure, boarders can still slip past your supershields, but at least there's an explicit in-universe justification for it now. You can get said augmentation for your own use as well, so it's no longer a case of computer cheating.
4* SugarWiki/AwesomeMusic: [[http://benprunty.bandcamp.com/album/ftl Heck, just have a listen for yourself.]]
5** The [[http://benprunty.bandcamp.com/track/engi-explore Engi theme]]. On the sector map, it is an extremely sedate (if tense) piece, one which is difficult to imagine overlaying anything over it to produce a battle theme. Yet like the other themes of the VariableMix, [[http://benprunty.bandcamp.com/track/engi-battle it does just that]]. That alone is grounds for awesome, but the Engi battle theme is also one of the best in the game.
6** [[https://benprunty.bandcamp.com/track/slug-battle Slug Battle]] has a nice war-drums feel with shouting vocals.
7** [[https://benprunty.bandcamp.com/track/cosmos-battle Cosmos Battle]] has a low synth riff with a very similar tempo to Guns N' Roses Locomotive.
8** [[http://benprunty.bandcamp.com/track/last-stand Last Stand]] is that kind of piece to get you pumped to go out and rip that Flagship to shreds.
9** [[http://benprunty.bandcamp.com/track/bonus-federation Federation]]. It was cut due to not sounding climatic enough for the [[FinalBoss Last Stand]], but it's still a great track in its own right.
10** It's a CutSong, but [[http://benprunty.bandcamp.com/track/bonus-horror Horror]] does its goal of setting a creepy atmosphere very well. ''[[GoneHorriblyRight Too]] [[NightmareFuel well]]'', as Ben Prunty mentions in the liner notes.
11** The ''Advanced Edition'' [[https://benprunty.bandcamp.com/album/ftl-advanced-edition-soundtrack songs]]!
12** Colony Ship stands out, it's an older 8-bit song from 2008 but not only is it catchy, it provided the RecurringRiff, the "Milkyway Melody" for this game alongside the "Conflict Theme" and 'Space Cruise Chords".
13** The success of the ''FTL'' soundtracks led Ben Prunty to create a SpiritualSuccessor album, ''[[https://benprunty.bandcamp.com/album/deep-space-deluxe-ep Deep Space EP]]'', a mini-album of three tracks each with the same Battle/Explore format of the ''FTL'' tracks.
14* BetterOffSold:
15** Many 3-power and 4-power weapons can be hard to add onto a weapons loadout, since they take up a significant fraction of the maximum of 8 power in the weapons system, requiring many weapons upgrades (let alone the cost of purchasing the weapon itself). Thus, if you receive something like a Burst Laser III (4 power, 19 second charge time, 5 damage at most) or a Breach Missile (3 power, 21 second charge time, 4 shield-piercing damage), it's often easier to just sell them to a store for a decent chunk of scrap rather than try to fit them into a loadout.
16** The two small utility bombs, the Stun Bomb and the Lockdown Bomb, have very little effect when you aren't boarding, and are only marginally better when you are, making them prime sell material.
17** Most augments are at least slightly useful, but few provide a large effect compared to selling them for scrap at a store. The most noteworthy examples are Advanced FTL Navigation (allows you to jump to any previously-visited beacon... which will be completely empty, thus spending a fuel and wasting a tick forward of the advancing fleet), and Repair Arm (which [[CastFromMoney takes a percentage of your money to heal you]] every time you get money, when you'd rather keep the money to upgrade your ship so you get hit less). While not entirely useless, these are often viewed as something to immediately sell at the next store.
18* DemonicSpiders: See [[DemonicSpiders/FTLFasterThanLight here]].
19* FanNickname:
20** ''FTL: [[NintendoHard For The Lose]]''
21** A specific type of slug ships (slug scouts) are known as "[[ArmoredCoffins coffin ships]]" due to [[TooDumbToLive their oxygen system being separated from the rest of the ship and hence impossible to repair]], leading to easy crewkills.
22* {{Fanon}}:
23** Not many fans depict the FTL engine as a jump drive (essentially, the ship teleports), and many interpret it as either a warp drive or a hyperdrive, so as to get some downtime that doesn't involve sitting around nav beacon 180,000,000 doing nothing.
24** Quite a few people have the Flagship's AI as the Rebellion's Commander-In-Chief.
25** The Flagship's beam gunner (since beams can't harm you unless the shield is down) is considered a double-agent due to the strategy of leaving them alive to prevent the AI from taking over.
26* GameBreaker:
27** Teleportation, so long as you have even a moderately competent boarding party, quickly builds up scrap thanks to the increased rewards from boarding, gives some of the best victory options, and requires minimal to no assistance from your ship unless they have a medbay/clone bay. Your ship only needs to be able to resist the enemy's attacks until the crew is dead. It's more difficult to use against automated ships, but it's still so powerful that winning ''without'' a teleporter and boarding party verges on a SelfImposedChallenge.
28** The Weapon Pre-Igniter plus any of a half-dozen powerful weapons with a long charge time as their NecessaryDrawback. Being able to open fire the moment a fight starts typically lets you crush any opponent who isn't completely immune to your arsenal. Even the final boss is a lot easier to beat thanks to being able to shut down some its more powerful abilities on the spot. There's an achievement for destroying an opponent outright with this ability.
29** Similarly, Automated Reloaders augments. They stack, so that with a fully-trained crewmember on weapons, you can slice the charge times of all your weapons by ''half''.
30** The Rock Cruiser Type B, "Shivan". It has Rockman plating and four Rockmen crew by default, making it very tanky and resilient to boarding. Its Heavy Pierce Laser can dominate early sectors, as it charges fairly fast, ignores one layer of shielding, and does as much damage as an Artemis missile without using ammo or being countered by Defense Drones. It also comes with Fire Bombs, which in of themselves are fairly useful due to their ability to set fires and hurt enemy crew while ignoring shields. Once you install a teleporter however, the combination of a fireproof Rockmen boarding party with Fire Bombs will essentially allow you to easily defeat any ship that isn't a drone, or crewed by Lanius.
31** The Crystal race, though [[PurposefullyOverpowered their Game Breaker properties are justified]] by the [[ThatOneSidequest sheer difficulty]] involved in [[LuckBasedMission unlocking them]]. [[spoiler:Their lockdown ability prevents entry and escape from a room, which can be used to contain enemy boarders, trap enemy crew inside a room, or prevent them from accessing a room while you hammer away at its occupants and systems. Extra hp allows them to defeat most opponents (excepting Mantis, Rockmen, and Anti-Personnel/Boarding Drones) without suffering any drawbacks save for a slightly reduced movement speed]].
32*** Their ships are also quite powerful as well. The Type B rivals the Mantis as the premiere boarding ship of the game, starting with [[spoiler:three crew members, as well as a four-slot teleporter located right next to a medbay. The Type A is no slouch either, possessing weapons that bypass one layer of shielding, don't require ammo, and have a small chance to cause hull breaches]].
33** The Mantis Cruiser Type B "Basilisk", with its starting 4-man teleporter, defence and boarding drones, and level 2 shields. It doesn't come with weapons, but you do not need them. There are only two types of ship it cannot beat outright, one of which is easily corrected once you've got some scrap to upgrade your teleporter one level. Almost every encounter can be won simply by beaming over your entire crew to kill off the opposition while your shields and drone soak up any damage they can do. This also gains a lot more scrap than blowing ships up, making it much easier to improve the ship. For AI ships, you can use your boarding drone to destroy systems slowly (AI-Scout) or a combination of the level 2 teleport and drone (AI-Assault). With all that extra scrap, you can easily buy weapons to disable ships you can't kill by boarding. By far, this ship is the easiest one to get to the endgame with because it affords a considerable early game advantage. Its only disadvantage is Zoltan ships, which can't be breached with the teleporter while their shield is up (unless the RandomNumberGod blesses you with a special bypass augment).
34** Breach Bomb II, which tends to wreck entire ships in one well-placed burst if it hits. Because it does damage to crew members and opens holes in the ship, this can be used over and over to disable most any ship save for Slug ships without destroying it. This even works on the Flagship; repeatedly applying the Breach Bomb to the medbay in the first stage can lead to the entire crew dying painfully, leaving it open for a boarding party to disable during the other stages. Finally, AI drones and the Flagship's last-resort AI don't repair breaches, and breaches in system rooms need to be repaired before any system damage can be repaired, so any system damage in a breached room will never get repaired, leaving them permanently disabled (unless you jump away and then come back later).
35** Ion Blast II. Capable of firing faster than a system can shrug off its effects, it only takes a few quick salvos to take down even level 4 shields, making it an ideal complement to beam weapons. With another ion weapon or a stack of Automated Reloader augments, you can keep two or more systems indefinitely suppressed, allowing you to eliminate your opponent at your leisure, whether by firing up another weapon or targeting their oxygen system. Its rate of fire and nonlethal nature is also excellent for leveling up your crew's Weapons skill. The Engi A ship starts off with this, and while difficult to do so, it can use this and its Mk. I Attack Drone alone to destroy the Rebel Flagship.
36** Mk. II Attack Drones. While they cost the normally excessive 4 power to use, they fire much faster than a Mk. I, take only half the space to use, and, if you can manage to get your hands on two of them, [[http://imgur.com/a/RMbKL can basically defeat the final boss on their own]]
37** ''Advanced Edition'' adds the hacking and mind control subsystems, which completely unbalance the game. Forget needing a teleporter, just launch a hacking drone at the oxygen and suffocate the ship, or use mind control to make the crew kill each other. The downside of course, is that it's almost as easy for the enemy to do this to you with the same.
38** The Lanius B Cruiser gives you a clonebay, mind control, a teleporter, an advanced version of the Flak Mk 1 (only cost 1 energy to operate ''and'' has lower recharge time to boot) and ''two Lanius'', who drain oxygen from rooms. If you can't be hurt by the enemy, then it is a trivial matter to use the flak to destroy the enemy oxygen room, teleport the Lanius in, fight for however long it takes to drain the oxygen out of that room, followed by the rest of the ship soon enough.
39** Also from ''Advanced Edition'', the [[GatlingGood Chain Vulcan]]. It's extremely rare, starts by firing one shot every 11 seconds, and takes 4 power, but it is the ''only'' weapon you will ever need to destroy anything. The time between its shots drops by two seconds with each firing, so eventually it fires 1 shot per ''second''; the fastest enemy shields will recharge is 1.5 seconds. Battles are reduced to setting the Vulcan to autofire on the shields and breaking it apart, then destroying enemy systems at your leisure and occasionally reminding the enemy crew the futility of repairing the shield with another shot. Not even several misses in a row can stop the onslaught for more than a brief moment.
40** If you are lucky enough to find a zoltan shield along with a cloak, your defense will be boosted to such a ludicrous amount that it becomes possible to destroy the flagship [[CurbStompBattle without even taking a single hit]].
41* GeniusBonus: A couple of the ship names qualify. ''Ariolimax''[[hottip:*:Type C Slug Cruiser]] is the genus for banana slugs, named for their yellow coloration. The corresponding ship palette is also a bright yellow color. Likewise, the ''Nesasio''[[hottip:*:Type A Stealth Cruiser]] is named after a genus of owl, a kind of bird known for being silent and stealthy.
42* GoddamnedBats:
43** AI Controlled Scouts when using the Mantis Cruiser B. No weapons, you have to send over a boarding drone to very slowly blow up each of the ship's systems, wait until they repair a few times, and then finally the drone will blow up the ship for measly scrap, often less than 10 value on Normal.
44*** Auto-Scouts also have the nasty habit of trying to FTL escape to inform the Rebels of your position, making the Rebel army advance faster if they succeed in doing so. In an amusing contradiction, however, if ''you'' jump away first, this doesn't happen.
45*** Auto-Scouts in later sectors tend to have stupidly high evasion. Coupled with multiple layers of shielding, firing a volley of 8 shots and ''still'' failing to land a shot is not unheard of. This, like the above problem, can be solved with the use of the Hacking system targeted at their engines, but it can be seen as a waste of a drone part to take out an AI ship.
46** Slugs in general, with their system-disabling shenanigans. Add in that they live in nebulas, which people already tend to avoid for their sensor-disabling annoyances and the aforementioned plasma storms, and you get one really annoying race to deal with.
47** Ion weapons, especially either Ion Blasts or Ion Bombs.
48*** Ion Intruder drones in the Advanced Edition combine ion weapons with boarding drones. While not as dangerous as boarding drones due to their lower durability and inability to cause direct damage, they absolutely love to stun vital crew members or disable important systems at the worst possible moments.
49** Cloak tends to prolong most battles it's in. Usually, the only dangerous enemy that has cloak is the Flagship. Most of the other times, all it does is waste your time.
50** Zoltan ships with Zoltan Shields, if you do have weapons, primarily due to the extra time needed to eat through them.
51* GoodBadBugs: The new features of ''Advanced Edition'' have some possibly unintended effects on achievements, making them far easier to unlock.
52** "The guns... They've stopped" requires using the Engi ship to simultaneously cause ion disruption to four different systems. Normally this would require at least two ion weapons. However, with the addition of pulsar nodes, the ion burst can potentially knock out enough systems to let you earn the achievement with only one ion weapon.
53** "Avast, ye scurvy dogs!" requires you to kill five enemy crew using the Mantis ship without taking hull damage or having any of your own crew die. While that many crew don't become common until late in the game, cloned enemy crew count toward the total, making it much easier to get the achievement in an early sector if you can find one with a Cloning Bay.
54*** Mind Controlled crewmembers are treated as AI-controlled members of the opposing crew. A controlled enemy is treated as one of your own crew, and as such you can use a Teleporter to "return" them to your ship... where they are easy pickings for your crew once the Mind Control wears off.
55* ItWasHisSled:
56** The Crystal race is supposed to be a WalkingSpoiler, but the [[LuckBasedMission heavily luck-based requirements]] to unlock their sector and ship are [[ThatOneSidequest so notorious]] that virtually nobody treats them as a spoiler.
57** Similarly you're not supposed to know anything about the [[FinalBoss Rebel Flagship]], but nobody cares about the spoiler factor of it.
58* JunkRare: The ''Crystal Vengeance'' augment is pretty useless. 10% chance of counterattack that deals 1 damage every time your hull is damaged sounds lame, and it ''is'' lame. However, they sell for quite a bit and can give a significant early scrap advantage, in addition to the GameBreaker status of the Crystal ships.
59* LowTierScrappy:
60** The Engi type-B layout is disliked on account of the fact that it has only a ''single'' crewmember, which becomes problematic if boarding parties appear and the player hasn't been able to hire or otherwise receive a new crewmember (and due to the RNG-based nature of each run, that's quite likely). Its weapons also leave much to be desired: A Heavy Ion and a Heavy Laser, which by themselves are incapable of harming any ship with just two shield layers or more, while the most of other ships at least have some way of dealing with multi-shielded enemies right off the bat (such as missiles, the Engi A's ''much'' faster Ion Blast II, or multiple laser weapons). This more or less makes players call it a "hard mode" ship minus the [[DifficultButAwesome "awesome"]] or [[MagikarpPower latent potential]].
61** As far as crew examples go, [[PunyEarthlings humans]]. In the original version, they trigger no blue events, [[MasterOfNone have no special abilities]], and are only effective in combat when against Zoltans or Engi, and will lose to the former in ''Advanced Edition'' thanks to Zoltans exploding upon death. Slugs have the same stats as humans, but also have telepathy (which was further improved in Advanced Edition) and can trigger blue events. The Advanced Edition mercifully gave them [[HumansAdvanceSwiftly slightly faster skill progression]] and a new blue option, but it still doesn't really save them in the eyes of most players and they tend to be the first crew to be kicked out of a full ship in favor of races with more specialized abilities.
62* MemeticMutation: [[GiantSpider Giant alien spiders]] are [[SeriousBusiness no joke]].[[labelnote:Explanation]]One random event features a ship crew under attack by giant spiders. This is the first option, word-for-word. It also has a high chance of eliminating one of your crew members. Hence, giant alien spiders are no joke.[[/labelnote]]
63** Upgrade your engines! [[labelnote:Explanation]]Upgrading the engines of your ship is a good way to take less damage, so, on the subreddit, it has become somewhat of a catchphrase to berate failed builds if it did not have sufficient engines. It has gotten to the point there is a CargoShip between the subreddit and engines.[[/labelnote]]
64* MinimalistRun:
65** The Zoltan Cruiser achievement "Manpower" requires you to get to sector 5 without upgrading your reactor.
66** Federation Cruiser achievement "Artillery Mastery" requires you to get to sector 5 without upgrading your weapons system, excluding the artillery system of course.
67** The game has several achievements gained this way, like surviving to sector 5 without buying anything at a store, never purchasing repairs, or never upgrading your reactor.
68* SugarWiki/MomentOfAwesome: Any time you and your crew help out an NPC in desperate need and save the day in triumphant fashion. After a bad run where you had to refuse help to almost everyone you met, it feels liberating to blast the pirate scum and save the innocent refugees the next time around.
69* SugarWiki/MostWonderfulSound:
70** The little sound when the shield recharges to the right level just in the nick of time, or the little FTL jump ready chime when you ''really'' need to escape.
71** The sound of air escaping when you deliberately open the air locks to put out a fire or defenestrate an enemy boarding crew as they fruitlessly attempt to pry open your blast doors.
72** The sound of your cloak activating, followed by "whoosh whoosh whoosh whoosh whoosh" as your enemy whiffs his shots.
73** [[http://benprunty.bandcamp.com/track/victory Victory]]. Whether it's your first time and you've just scraped through by the skin of your teeth, or you're an ''FTL'' veteran, hearing this is sure to make your heart leap.
74** The sound of getting an achievement, usually followed by the sound you get when unlocking a ship.
75** The cashier till sound that plays when you buy something from a store, particularly fuel or repairs.
76** The low-pitched ''ding!'' that plays when one of your crew has upgraded one of their skills.
77* NightmareFuel: The game is thankfully light on graphical depictions of violence, though the game still has its [[NightmareFuel/FTLFasterThanLight scary moments]].
78* NoCasualtiesRun: Acknowledged by the game; reaching Sector 8 with no crew losses unlocks the "No {{Redshirt}}s Here!" achievement.
79* PlayerPunch: There is a chance to find a rebel ship refitted for transporting goods to civilians in need during the war, [[VideoGameCrueltyPotential and you can steal the supplies from them. Or destroy the ship.]] [[BreadEggsBreadedEggs or both.]] [[http://ftl.wikia.com/wiki/Rebels_Supplying_Civilians The game can and will call you out on it.]]
80--> ''(If you steal their supplies)'' "This is why the Rebels will always have support!" \
81''(If you don't steal their supplies after fighting the Rebels)'' "My son was on that ship. He only helped the Rebels because they cared enough to help us. Without him to find us supplies, we'll likely be forgotten and die out here."
82* PlayerTic: Players defeating the flagship via the "kill all crew except the laser gunner" method will often finish it off by firing an AlphaStrike [[CoupDeGrace at the remaining crew member]].
83* PolishedPort: The iPad port runs smooth as silk and has a number of interface tweaks to accomodate the use of a touchscreen, allowing you to enjoy the same game on a device about the size of a sheet of paper. And it has both the vanilla and ''Advanced'' editions.
84* ScrappyMechanic:
85** Some players feel the game is a bit ''too'' reliant on RNG, so winning isn't satisfying because it feels like it's because the game "let" you win. Case in point: In one run, you may end up finding four Burst Laser II's, allowing you to cheese the FinalBoss with 12-shot [[BeamSpam laser spam]]. In another run, you may be stuck with default weaponry or at the least ineffective weapons at stores that prevent you from damaging the flagship at all unless you also invest in a teleporter or hacking system (provided, again, that you manage to find a store that sells them).
86** Sometimes the text options are a ViolationOfCommonSense. To give one example, you might have to choose whether to let a seemingly insane person on board. You will either lose a crewmate or gain the one you let on board as a crewmate, with nothing indicating which outcome will play out. Thankfully, there are occasionally options highlighted in blue which help you no matter what.
87* ScrappyWeapon:
88** The Burst Laser Mark III fires [[MoreDakka an impressive five-shot barrage]], but players generally [[AwesomeButImpractical avoid it due to its high power requirements and long charge time]], and because the same amount of firepower can be easily achieved by firing several cheaper lasers at once.
89** The Glaive Beam can do massive damage on enemy ships with tightly-arranged rooms, but it takes a whole ''25 seconds'' to charge, or about 23 with a crewmember with no improvements to weapon skill. And like the Burst mkIII, it uses four bars of power; an unlucky hit can shut that beam off very easily. This is part of why getting out of the first few sectors with the Stealth B ship is quite hard (along with that ship having no shields to start with), as it is the ''only'' starting weapon of that ship and only has enough power in weapons to power the beam (no extra power slots to act as a buffer).
90* SelfImposedChallenge:
91** One particularly crazy one involves using absolutely no oxygen on your ship at all (without having any Lanius crew). You'd think everyone would quickly die from asphyxiation, but apparently a level 2 Medbay completely nullifies the damage taken from asphyxiation. It's still ridiculously difficult, since the Medbay is only so big, and you need someone at the helm to jump the ship from point to point. [[https://www.youtube.com/watch?v=GNHfxwbETaM It's been done]], however crazy it sounds.
92** Some people think that Engi Cruiser B or Stealth Cruiser B are also "hard-mode" ships. Engi B has a single crewman, no sensors, and has drones take care of boarders and ship repair; one could take it a step further and go for a SoloCharacterRun, never hiring a single new crew member (and if any are picked up for free, [[VideoGameCrueltyPotential kill them by asphyxiation]]). Stealth B has no shields and starts with only one weapon: the incredibly slow-charging but powerful Glaive Beam.
93** [[http://www.reddit.com/r/ftlgame/comments/17aptb/bizarro_mantis_b/ Someone was crazy enough to build up an all-Engi crew...with the Mantis B.]] Then crew members get slaughtered. ''Enemy'' crew members.
94** Destroying all of the Rebel Flagship's crew will trigger its auto-repairing AI. Here's an idea: Approach the Flagship and then kill the entire crew before doing any other damage.
95** Try beating the game without pausing.
96* StopHavingFunGuys: To some players, playing on Easy is a felony.
97* SuspiciouslySimilarSong: "Lanius (Explore)" has a melody that sounds a lot like Music/CarbonBasedLifeforms' [[https://carbonbasedlifeforms.bandcamp.com/track/mos-6581-album-version "MOS 6581"]].
98* TearJerker:
99** Winning the game by destroying the [[FinalBoss Rebel Flagship]] but [[MutualKill getting your ship destroyed or crew wiped]] in the process. [[HeroicSacrifice Your crew is hailed as Federation heroes, but they don't live to witness galactic freedom.]]
100** Pretty much any event in which you try to help someone in need and end up dead, or have to refuse to give them help because you simply can't risk it. The game pulls no punches in dropping the guilt on you either; expect your crew to stare at you in sad shock as you radio that burning space station to tell them you can't save them.
101** The state of the Federation and the universe over the course of the game. A noble collective of many different alien races peacefully co-operating for the greater good of the universe, the Federation seems like an ideal government. And yet it's on its last legs after a brutal war caused by a group of what appear to be violent human-supremacists. Add to that the fact that pirates, slavers and killers run amok in pretty much every star system and it really paints a bleak picture of people's inability to get on.
102* ThatOneAchievement:
103** Ancestry, which requires you to go through ThatOneSidequest in the Rock Cruiser. That said the Rock Cruiser has blue options that make it slightly easier to complete:
104*** If you intend to do it in the Type A, get non-missile weapons as soon as possible (see DemonicSpiders above).
105*** If you intend to use the Type B, you need to complete two other hard (but still much-easier-than-this-one) achievements in the Type A to gain access to it - which involved destroying an enemy ship which has a defense drone using ''only missiles'' (alright, you start with only missiles, but defense drones are... designed to block them, and ships that field them often have the crew or repair drones to keep their drone control online), and killing an enemy crew in a room which is on fire (which is hard because you need to set a room on fire, then board it and kill an enemy crew member there - and the enemy crew members are programmed to flee from burning rooms if they can).
106*** Type C is slightly easier because you start with a Crystal crew member, allowing you to skip the first two steps of the quest. But you still need to complete the requirements for Type B as well as beat the flagship with it, find the Rock Homeworlds sector in the first place (very much not guaranteed) and then find the beacon allowing you to complete the quest (which in this case will be unmarked).
107* ThatOneAttack:
108** Missiles in general are much hated by just about everyone without a defense drone. It's not that they're powerful (early on they do one or two damage a pop), it's that they pass through shields. Worse still, they charge fast enough that you can pretty much guarantee the enemy will fire at least one before you stop them. Just to be clear, there's a good 75% chance that any given enemy, especially in the early sectors which only get a limited loadout to choose from, will have a missile launcher. Later in the game, enemies can field larger missiles that do as much as four damage per hit, but they mercifully take longer to charge and you'll probably have a defense drone by then, as well as high evasion and possibly a cloaking system to help avoid them.
109*** The flagship's triple missile launcher is notorious for this reason. At best, a single defense drone of any make can take down two missiles, and while you can cloak to dodge them, this only works every other time due to the longer cloak recharge. Unless you're fast with your teleporter or have a bomb/missile of your own at the ready, odds are a missile is going to connect. On the final stage, it's practically a guarantee since the Zoltan shield takes so long to get through.
110** Boarding Drones will cause a breach in whatever room they land in and wreak havoc until you take them out (or the drone control system). Considering they are immune to asphyxiation, has a Rockman's health and Mantis' damage, this is easier said than done. And of, if you manage to take them out, the enemy most likely will send ''another one''. Considering that the Rebel Flagship has both missiles and Boarding Drone, getting a Defense Drone is almost mandatory to complete the game. Previously, the enemy can send the drone without cooldown (although limited by the number of drone parts), almost ensuring that at least one will get through. ''Advanced Edition'' added a cooldown on their launching, making them slightly easier to take care of.
111** The hacking and mind control subsystems in ''Advanced Edition''. The hacking drone can be fired at any system and reverses the function of the system or subsystem it hits (oxygen drains, medbay damages, weapons and shields lose charge, engines/piloting are shut off). Not only that, the room it hits is locked down and has to be broken into. It also doesn't suffer from the drone-cooldown added to prevent drone-spam, so your enemy is going to fire it like it's a machine gun until they hit you or run out of drones. The mind control system co-opts one of your crewmembers and causes them to turn against you, usually attacking whoever or whatever is in the room with them. This can potentially shut off your ability to dodge or damage critical systems. In both cases, you can only hope you can knock the system offline before it does too much damage. On the plus side, these two are every bit as gamebreaking under your control.
112** The flagship's first power surge, the drone swarm, is possibly the single most damaging attack in the game. If your shields go down for even a second, you WILL be feeling the pain. It's not an exaggeration to state that if this pierces your defenses and takes out a vital system (like shields), you will probably lose. It also has a tendency to sync with the triple heavy lasers connecting with your shields or the triple Leto missiles firing. You'd better pray that their Halberd Beam isn't also up.
113*** The flagship's bigger attacks practically make it mandatory to have an evasion stat over 50% (and/or a cloaking device) which you can never, '''ever''' let go offline, because you ''will'' die if your evasion is turned off. You also better hope the boarding drones in the second stage land somewhere other than your cockpit, or that your defense drone can shoot them down repeatedly until the flagship's supply runs out.
114*** The flagship got ''even cheaper'' with ''Advanced Edition''. The first round comes with a hacking subsystem which can completely throw you off your game if it hits a vital system like weapons, shields, or engines/piloting, and will repeatedly fire until it connects or runs out of drones. The third round gets the mind control system hidden behind the massive Zoltan shield, which means you'll have a crewmember running around under enemy control for a significant period.
115** For Zoltan-Shielded ships, all flavors of anti-ship drones will quickly tear through all five points of Zoltan Shields, negating whatever advantage could be gained from it.
116** ''Advanced Edition'' adds an event where a Rebel AI ship hacks your shield system, reducing it by a point, and this can happen in the first sector. In other words, you have no shields for that battle. Worse, this ship usually gets a combat drone as a package deal, meaning you have to spend the next ten or so seconds getting smacked around by a drone while praying your weapons get enough time to charge. It's not an exaggeration to say that you can die by no fault of your own thanks to this event, because certain ships simply have no way to counter it.
117* ThatOneDisadvantage:
118** Shieldless ships. Only four ships don't start with laser and beam-repelling shield systems and while they have alternatives (a cloaking system in two cases, a special single-use shield in the third, and a special drone that periodically charges up one layer of a that same normally single use shield) they can be rapidly picked apart by anything with a beam drone (attack drones fire constantly for low damage which shields would normally absorb, but which adds up, and beams can't be dodged).
119** The Repair Arm augment. Any moderately savvy player knows to ''never'' buy this piece of garbage, since it steals 15% of your scrap to do something that is both cheaper at a store and which should at best be occasionally necessary if you know what you're doing. What makes it fit this trope is that you can be [[PowerupLetdown "awarded"]] the augment as part of a random event, forcing you to rush to a store to dump the thing. Depending on how far along you are, this can either be a small scrap gain, or a small to moderate scrap loss. [[RescuedFromTheScrappyHeap Slightly improved]] in the Advanced Edition, which buffed them by directly connecting the repairs to the scrap earned--so you can be healed more than once at time if you get a double-reward beacon and the scrap reduction stops when you're already at full health.
120%%** The Slug B cruiser.
121* ThatOneLevel: Primarily dependent on your ship and equipment. Several come to mind:
122** Nebula sectors for ships that do not have Long-Range Scanners, due to Ion Storms.
123*** Slug sectors, which are a subset of nebula sectors and often have events where your ship's systems get disabled, or reduced in effectiveness if you had the foresight to upgrade them.
124** Ships that do not start with weapons should avoid Zoltan sectors until they get a few, as Zoltan Shields block teleportation (assuming they didn't buy the Zoltan shield bybass sugment).
125** Rebel sectors are generally difficult for all ships due to the onslaught of Rebel ships, which include drones that can't be easily destroyed by boarding methods and often have high evasion. In ''Advanced Edition'', Rebel nodes come with Anti-Ship Batteries, making getting caught by the fleet [[SequelDifficultySpike even more dangerous]].
126** The "Unidentified Cruiser" is a GameBreaker for a reason. Many players take dozens of attempts before they get a run that gets the very specific, [[LuckBasedMission luck-based]] order of sectors that allows the sidequest to be finished.
127** To a lesser extent, unlocking the Rock Cruiser Type B, which requires completing two out of three Rock Cruiser achievements:
128*** The Ancestry achievement is the same thing as hunting down the Crystal sector, minus acquiring the Crystal Cruiser.
129*** At the least, the Defense Drones achievement is simple--just find a Rebel Rigger with a Defense Drone and then use [[MacrossMissileMassacre missile]] {{Alpha Strike}}s to prevent the Defense Drone from being able to shoot both missiles.
130*** The "Is it warm in here?" achievement requires killing a crew member of an enemy ship in a burning room, which is not easy because this requires a Teleporter and a way to start fires. Most weapons only have a low chance at best, and it's not uncommon to never find the Fire Beam or Fire Bomb, and even then Fire Bombs use missiles and can miss, while the Fire Beam requires that the enemy ship's shields be down first. Oh, and [[SpitefulAI enemy crews retreat from burning rooms at low health]], requiring you to time your attacks correctly so they get their last points of health beaten down before they can escape the room. And finally, the crew member ''must'' die from one of your hits; if the fire whittles them down to 0 HP, ''it doesn't count!'' You can guarantee this achievement by getting to the Rebel Flagship with a Fire Bomb in tow and using it on one of the weapon rooms, but it still takes a bit of a while to get there. ''Advanced Edition'' makes this somewhat easier if you have the hacking module, as that can be used to lock down a room and then kill the occupant.
131*** Ironically, killing a fellow [[ImmuneToFire Rockman]] can be easier way of getting the achievement. Rockmen are immune to fire and thus 1) don't flee from it, 2) fire can't steal your kill. Of course, this still means fighting [[StoneWall the tankiest race in the game]] in hand-to-hand combat, but at least it's more straightforward.
132** Pulsars heavily ionize two systems on both ships, and if shields are acive, one of the two affected [[OhCrap will always be shields]]. The result is a mad dash to destroy your opponent before it scores heavy damage on you. Oh, and you better pray that [[FromBadToWorse the other affected system isn't weapons]]... Of all environmental hazards, pulsars are by far the most likely to outright end your run if the RandomNumberGod has decided to screw you over.
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