In what order do weapons fire?

All of your weapons will start firing at the same time if you trigger them at the same time. Each weapon will arrive depending on the speed of the projectile and the firing delay of the weapon. The arrival time of projectiles is modified very slightly depending on where it is on your ship: weapons mounted at the bow will arrive faster than weapons mounted on the wings, because they have slightly less distance to traverse.

According to the weapons table on the wiki, the projectile-based weapons fire at roughly two speeds: laser weapons are fast, and ion and flak weapons move at a little over half that speed. Beam weapons, on the other hand, are nigh-instantaneous: they hit at the same time they fire. Bombs have a specific delay: after being fired, there's a short time until the bomb appears on the ship, and then another delay before it explodes.

Imagine you have the following weapons on your ship (ignoring, for the moment, that this configuration is impossible):

• Pike Beam (1 damage beam weapon)
• Ion Bomb (4 damage ion bomb)
• A Heavy Laser I (1 damage to shields, 2 damage to hull/system)
• A Flak Gun I (3 damage, with poor aim)
• A Heavy Pierce I (2 damage, ignores 1 shield)
• A Burst Laser I (2 shots of 1 damage each)
• A Hermes Missile (3 damage)

Your opponent has level 3 shields: they will avoid 3 shots of damage, and the shield system has 6 health (though it will cease generating any shield once it has taken 5 damage).

In a perfect world, you want the shots to arrive in the following order:

1. Ion Bomb on the pilot to prevent evasion on everything else (For the sake of this example, assume it hits.)
2. Hermes Missile on the shields
3. Heavy Pierce I on the shields, ignoring the last shield and reducing the shields to 0
4. Everything else, to do unspeakable damage to whatever's left

You trigger the weapons in the following order, unpausing briefly between each shot:

1. Ion Bomb
2. Hermes Missile and Flak Gun I (just after the Ion Bomb arrives, to guarantee that the Ion Bomb will explode before the Missile can arrive and be dodged). The Flak Gun I would normally hit the shields, but flak projectiles are slow and will get there after the shields are down from the Heavy Pierce I in a moment.
3. Heavy Pierce I, after the Missile leaves your ship but before it arrives. You must damage the shields before the Heavy Pierce shot even touches the shields.
4. Burst Laser I and Heavy Laser I, after the Heavy Pierce I leaves your ship but before it arrives. You must damage the shields before the laser shots even touch the shields.
5. Pike Beam, only after you see the shields go down. The beam will hit nigh-instantly.