continued
Defences come in 3 types, EW, the subtle kind, armor the less subtle kind and shields, the obvious kind.
Shields have a set amount of HP, depending on the type, when broken they remain down for an amount of time, depending on the quality of the shield, before being restored at full hp.
They are a great way to make your ships tougher against stray fire, but won't cut it if the enemy is focusing on your ships with real firepower.
They also tend to take damage a lot faster than the ship itself, since they are bigger than the ship and won't deflect anything.
Some shields, deflectors, disruptors and graviton, can't be broken no matter how much fire they take, but these types block only some certain types of attacks, depending on the shield. The most important is the deflector, which is immune to kinetic and missile damage, but has no effect on any kind of energy weapons.
Against all kinds of shields, prioritize hitting the targets bridge section, since the shield disappears when the section making it breaks.
Shields also require a section of your ship be dedicated to making the shield, so they will cut into the amount of firepower your ships have, and dreadnaughts are too big to be shielded, they can use deflectors though, and dreadnaughts cannot loose individual sections, so you can't just break the shield by shooting out its section.
Armor is your most important defence. It gives you a flat HP bonus to the section its on based on the armors quality, up to doubling the HP with adamantium.
Armor also improves the chance of incomming kinetic projectiles deflecting harmlessly, this scales up with quality and even low quality armor make massdrivers nearly unable to hurt you. The regular kind anyway, AP will also deflect, but not anywhere near as often.
Mirrored armor doesn't improve the sections HP, but gives a chance for lasers to deflect.
The last type of defence is EW. Jammers, wild weasels and the EW dreadnaught section.
Jammers make a sensor shadow around the ship, similar to big asteroids, stopping enemies from seeing what is under it on the tactical map, Its main function is to prevent missiles from homing in on any ship under the shadow.
Wild Weasels try to redirect enemy missiles that come nearby to themselves. If covered in PD they can protect an entire formation of ships from missiles and torpedoes. They also fill the tactical map around them with ghost targets, but this only works on players, not AIs. Both prevent the enemy from seing the number of ships in your fleets on the strategic map, making for easy decoys.
DN EW sections combine Jammers and Wild Weasels with another ability, they will redirect some of the missiles that target them back at the enemy. Not often, but it does happen.
Cloaking sections can also be used as a defence, but only the improved cloaking ones, as regular cloaking sections drop cloak when they fire, making your ship vulnerable.
Keep in mind that the AI with try to blindfire at the last place it has seen shots from your ships coming from, so keep your ships moving.
Stealth armor makes your ship invisible beyond visual range, so only to the tactical map, and does nothing once the enemy has a ship close enough to spot you visually. It doesn't give any deflection chance or HP either. Its only real use is strategically, as it lowers the range enemies can spot the fleet on, on the strategic map.
Advanced Sensors can spot cloaked ships, but not stealth armored ships nor beat jammers or wild weasels. DN EW sections also include Advance Sensors.
Personally I prefer to always have at least one ship in every fleet with advanced sensors, but the section is fragile and nearly unarmed, so don't put it on the frontline fighters.
PS
One last thing I forgot was Torpedo weapons. They come in 2 types, nonhoming, which work like a cannon with really long range, usually doing only very little damage, and the homing kind, which does increasing damage the longer it has travelled and do limited splash damage. AM torpedoes can hit insanely hard, allowing a ship with enough of them, to kill enemy cruisers, if they don't have too much armor, with one salvo. Liirian Assault/Barrage cruisers are very good for this kind of tactics, but it requires a lot of micromanagement of your targets or they will overkill the first thing they see and be left unable to shoot anything else for the next 30 seconds, just like missiles.
The homing torpedoes can be shot down, like missiles, but they are a lot tougher and thus harder for enemy PD to take down. Not sure if wild weasels can redirect them either.
The gimmick variant of the homing torpedoes does its damage over a fairly large area, but this is rarely enough to splash over multiple cruisers.
EMP torpedoes shut down enemy ships, the bigger the target the shorter the time, and come in guided and unguided variants.