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  • Just about every ship in the game has a certain strategy it's just not cut out to handle, at least until you somehow acquire the hardware and/or crew to make up for starting deficiencies. For instance:
    • Boarding parties, especially Mantis boarders or large 4-man groups, for ships that start off with small and/or combat-incompetent crews, which include:
      • The first two Engi cruisers (Type A has two Engis and a Human, Type B has just a single Engi), seeing as Engis do half-damage in combat. The Type A, however, has a Medbot Dispersal augment to help its crew in combat, and the Type B can be run almost completely depressurized (outside of the cockpit) once you get blast doors, and until you get extra crew, as its "crew" of internal drones don't need oxygen. Type C at least has a Lanius and a clone bay.
    • All three Zoltan cruisers. Due to their reliance on Zoltan crewmembers for power, relocating them to different rooms to fight off boarders may cause ship systems to lose power, resulting in weapons getting canceled, cloaks getting deactivated, shields dropping, etc. Their Zoltan Shield augment can prevent enemy ships from using their teleporters or launching boarding drones while it's active, but the Advanced Edition introduces a special augment that allows enemies (and the player) to get past it, and several random events involve its use. On the other hand, it also gave Zoltans the special ability to explode and damage enemies when they die, giving at least a little hope to the Zoltan Type C with its clone bay.
    • The first two Slug cruisers, but especially the Type B. It's not quite as bad for the Type A since Slugs can telepathically track the enemy boarders, and the Type A helps its two-Slug starting crew by being pre-equipped with blast doors. The Type B though has no starting medbay, and it depends on its Healing Bursts to keep its three-Slug crew alive, so if weapon systems go offline or you run out of missiles, you have no way to heal your crew.
    • All three Stealth cruisers. With no shields, evasion and cloaking are their main form of defense, and they need their systems to be manned more than any other ship. The Type A, though, has a crew of three Humans, while the Type B has two Humans and a Zoltan with only a two-square medbay. Boarding parties in your cockpit are bad for any ship, but are worse for the Stealth ships because you lose evasion and can take hits even when cloaked. The Type C gets a shield overcharger that creates a Zoltan shield, but it's only 1 bar of shield, it takes loads of scrap to upgrade the power system, and then to buy a shield.
    • To a lesser extent, boarders are also problems early on for the Kestrel A, the starting ship, which also has 3 Humans, and the Federation Cruiser B, which has a Human, a Slug, and a Zoltan.
    • The Rock B has no external doors, and the crew of four Rockmen are sturdy but very, very slow. If enemies board you, you cannot simply vent the room they're in, you have to chase them around with your crew. And your crew is so slow that any boarders will have probably destroyed a system or two by the time you finally catch up to them.
  • Attack drones and beam drones for any ship that doesn't have a proper shield system, seeing as the drones have higher damage-per-second than regular weapons at the cost of burst damage capability, and are hence particularly lethal against unshielded targets. This includes all 3 of the Stealth cruisers, and to a lesser extent the Type B Zoltan cruiser. The Stealth ships cannot conveniently cloak away from the almost continuous drone fire like they can with ship-to-ship weaponry volleys (not that the Stealth C can do that anyway), so hull damage becomes inevitable. With the Stealth A (Nesasio), you can still go under cloak early and try to take out the enemy drone control with your first volley. But with the Stealth B, you have to wait and suffer, and if your weapon systems are hit, your power-hungry Glaive Beam goes offline and your only option is to try and run. The Stealth C has it that much worse, as its only protection from drones is the fairly unreliable Anti-Drone and its slow-charging Shield Overcharger, as it lacks a cloak in spite of being a Stealth cruiser. The Zoltan B has temporary protection with its Zoltan shield but drones tend to tear through it fairly rapidly, but like a cloak, this still buys you some time to charge your weapons and try to disable the enemy's drone control. The Zoltan B also has it easier since it can acquire regular shields earlier than the Stealth cruisers can.
  • Zoltan Shielded enemy ships for any ship whose direct-damage offensive capability is either completely dependent on missiles (Rock A, Slug B), or just flat out non-existent (Mantis B, Unidentified B). A Zoltan shield takes five damage to knock offline, which is the equivalent of three missiles. That's basically one whole dead ship in the early sectors. And ships that start with no weapons at all have no option except to run, since the shield blocks out teleporters and boarding drones (Advanced Edition adds an augment that can bypass it, but getting that is hit or miss). Furthermore, the Zoltan Shield takes at least one round of combat to knock out, three if you're unlucky. For the Stealth B, which depends on One-Hit Kill tactics with its Glaive Beam to prevent (most) damage in the early game, that extra round is an eternity of vulnerability which can easily cost you the game.
  • Plasma Storms, a randomly occurring environmental effect in Nebula nodes. Running into one cuts your reactor output in half and depowers systems at random accordingly. This works on your enemy, too, but they can generally manage greater reactor output than you can. When you have to juggle power between your weapons, shields, engines, and life support, you can expect the enemy waiting for you to put some big holes in your hull before you make it out of there. Fortunately, having the Long-Range Scanners augment you can see the storms from afar and avoid them accordingly.
  • Boarding drones. They're essentially Rockmen boarders but with the attack power of a Mantis and an immunity to suffocation. They pass through shields and cause a hull breach in the section they impact, making it that much harder to kill them if they're attacking a system. Oh, and if you manage to kill one, the enemy will just send another, which will put another breach into your ship, unless you take out their drone control first or they run out of drone parts. If you get hit by one, hope it doesn't land anywhere vital and destroy the enemy's drone control before it causes too much damage. While they can be intercepted by defense drones, they're small, fly fast, and can be launched faster than missiles, and have a better chance of getting by as a result.
    • Zoltan Shields and cloaking can buy you some time to try and take out enemy drone control, if you have them, and Slug ships can automatically repair breaches, making them slightly less hazardous. There is also an option to just use upgraded oxygen system to pump in oxygen faster than breach drains it, but that only works with limited amount of breaches.
    • Advanced Edition implemented a cooldown on all destroyed drones that nerfs this significantly; now drones take about as long to recharge as an average missile, meaning that while it will take far longer to force the enemy to run out of them, neither can they spam them at speeds greater than you can counter. Sadly, the hacking system did not get this treatment.
  • Most of the time, Rebel AI-controlled Auto-Scouts and Auto-Assaults are Goddamned Bats. However, ships that lack direct damage weapons will find themselves largely incapable of doing anything about these ships. The Mantis B can defeat Auto-Scouts by launching a Boarding Drone at them and letting it destroy and re-destroy systems while the Auto-Scout auto-repairs them, but this doesn't work against Auto-Assaults because they're compartmentalized and hence prevent the Boarding Drone from moving around within them, requiring a very tedious and specialized method to destroy them without weapons. The Unidentified Cruiser Type B can't destroy them either until you find some regular weapons. And, to provide a challenge for any and all ships, sometimes in the late-game you can run into really dangerous Auto-Assaults, packing array of anti-ship drones, full batteries of four weapons, stupidly high evasion, and (rarely) up to five layers of shields. And since they're automated and depressurized, they can't be damaged by fire and have no crew that can be eliminated, so you're in for a long hard slog to try and bring them down.
  • If you're in a Slug nebula, then expect to run into many events where a Slug ship hacks your oxygen/medbay/doors/engines/various other systems, and then exploits your newfound weakness. If you haven't upgraded your systems enough to get a blue option, then you're in for a world of pain. Particularly nightmarish are the ones where they hit your oxygen, since that essentially puts you on a strict timer to either kill the ship or bail.
  • Any enemy ship with a medbay is this for the Mantis B, a boarding-oriented ship that doesn't start with any weapons. Enemy crew will simply retreat to the medbay at low health, and fighting in the medbay is pointless since the enemy can simply heal faster than you can damage them. Unless you've managed to pick weapons capable of hitting the medbay, your only hope is to get the crew to retreat to the medbay then cause damage to the shields (easier said than done, even with a Boarding Drone to create a distraction), since the AI prioritizes the shields over anything else, allowing you to take out the medbay. The Crystal B ship is also boarding-oriented with no weapons, but at least Crystals can beam into the medbay then lock it down until it's offline.
  • The ships in the Crystal Home Sector. They tend to show up with full arsenals of crystal weapons, which ignore one layer of shielding. Even worse, Crystals are very tough to kill, having boosted health and being resistant to suffocation. They can easily put a serious crimp in your plans to complete That One Sidequest.
    • Incidentally, those same ships can be quite easy if your ship is well prepared (which it should be, given Crystal Home Sector only appears in the lategame). Having 3-4 layers of shields, cloak and/or hacking makes Crystal weapons near harmless. Crystal shards are also interceptable by all defense drones.
  • Enemies with hacking capability can be this, depending on your loadout and where it hits (randomly assigned thanks to Artificial Stupidity). The worst is when it hits the weapons system of a player that relies on long-charge-time weapons (which can shut down your entire offense and make the encounter Unwinnable if you have no other way of destroying or disrupting the enemy hacking system), a non-upgraded O2 system (which drains oxygen far faster than a mere hull breach and can easily mean death for your entire crew if you can't destroy or disrupt the enemy hacking system or jump away fast enough), or a medbay when the enemy also has boarders attacking you.
  • Later in the game, Abandoned Sectors are dreaded due to one single kind of ship: Lanius Bombers. While scouts are easily dispatched, bombers are entirely something else: since they have no oxygen, they can have mind control, teleporters and cloaking at the same time (thankfully no hacking). You'll likely have to deal with many problems at the same time, especially if your weapons or shields are boarded, which, combined with the fact they tend to be quite well armed, make them a truely terrifying foe to face.

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