The gloves are off, the beam weapons are warmed up, the MAC cannon is ready to fire – and you're in control of everything. So what do you do, ace?
The simplest way to fight in space is to make sure that your ship is pointed directly at the enemy and to fire with as many weapons as you have available, as often as you can. It's not exactly a fine technique, but you should be guaranteed to hit with something. Spending time aiming at the target allows you to get a Lock-On, which ensures you hit with MAC torpedoes.
Your ship is not a ballerina, but some of your smaller enemies are graceful in space. If allowed to get close, they may be able to fly rings around your ship while blasting away at it. If you have point defense systems ready, you can worry less about these problems; otherwise you may want to launch battle pods, fightercraft, or the Falcon to assist in close-range defense. When confronting a much larger target (say, a starbase), you may want to be prepared to dodge volleys of fire by making an indirect course towards close range to avoid the dreaded bluespace artillery rounds.
Your primary weapons for ship defense are phase cannons, but the various weapons aboard the ship require Munitions Technicians (or occasionally other crew) to man and operate them. With a good Munitions Officer and Weapons Techs keeping your weapons loaded, you can bombard most enemies into oblivion with a few well-placed shots. The Deck Gun (NAC) in particular can punch holes through a ship if loaded heavily enough.
Weapons available (and their locations on the NARV):
These railguns accept 400mm teflon-coated tungsten rounds (or occasionally other ammunition invented by the boys and girls at R&D), which they launch via magnetic acceleration coils at terminal (and we do mean terminal) velocity, punching through the hull of enemy ships and opening them up to vacuum. The Railguns are kept in the Munitions Bay, with several crates of ammunition nearby and more available through the Automated Ammo Factory. Each railgun can hold up to ten pieces of ammunition in reserve plus one 'special' round. Each Railgun uses 500 kW at the moment it fires but does not have to sustain firing.
The AMS is an automated missile launch system that can be set in either Anti-Ship mode (target ships, particularly designated ships) or Countermeasure mode (target inbound projectiles). It will fire autonomously but requires reloading to keep firing. The AMS lives in the Munitions Bay and is loaded with the same missiles loaded onto fightercraft for compatibility. It can hold up to fifty missiles at a time.
The workhorses of the typical NovusCorp combat vessel, phase cannons modulate a plasma beam with a field jacket to ensure they can burn through shields and quickly strike at the hull and armor of a craft. The Phase Cannons share two rooms with the Torpedo Tubes. Phase Cannons require a power supply of roughly 200 kW to maintain rapid rates of fire, making them the most economical way to deal with smaller ships, and each bank can hold up to eight cannons at peak performance, if properly charged.
Torpedo tubes fire torpedoes, simply put, which must be assembled by the Ordnance Technician and distributed between the Torpedo Tubes and fightercraft. Torpedoes require little in the way of power (25 kW per tube), and the tube can hold five torpedoes at a time before requiring manual reloads. Available torpedo types include probe torpedoes, used to gather scientific information; shield-penetrating torpedoes; explosive torpedoes; high-explosive torpedoes; incendiary torpedoes; thermonuclear torpedoes; or decoy torpedoes, armed with anti-defense countermeasures to draw fire away from deadlier torpedoes.
These really big guns are, at their heart, nothing more than a really powerful rifle with a bullet that can punch a hole through a ship and detonate. These cannons use cannonballs, high explosive shells, and armor piercing shells to reduce ships to Swiss cheese from a long distance, assuming they are supplied with sufficient gunpowder, plasma accelerant, or other exotic materials. They cannot quite hit a target a planet away, not because there's air friction to stop a projectile in space once it's launched, but because it's very improbable that a target would be at the right place to be hit.
The Superliminal BSA is a massive machine which can accelerate a bolt of concentrated quark-gluon plasma to superliminal speeds, tearing clean through targets and annihilating everything in its path. It was developed from Bluespace Artillery cannons acquired in questionably legal ways. This powerful between-decks cannon has its controls on the Bridge, but its power supply is within the Munitions Bay. Operating it is simple, maintaining it is harder. It requires a massive amount of power just to fire even once. To input this power, simply go to its console, set a desired amount of incoming power, and enable charging. It requires 5 MW for one shot, so unless your ship is seriously overpowered don't expect to use this too frequently. This weapon actually can strike targets a planet away, or do massive damage to a planet, though it is difficult to do either and there are safeguards preventing you from attacking a planet without a valid target.
This builds standard missiles for loading into the AMS and the fightercraft.
This automatically churns out more Railgun ammunition.
This 'nuke 'em from orbit' weapon is the domain of the Requisitions Officer as far as loading and maintenance go, though the Overwatch Officer / Staff Officers can fire it. It can fire cargo pods, much like the Torpedo Tubes, or it can drop explosives, cluster bombs, antipersonnel fragmentation bursts, or thermonuclear torpedoes to rain fire and death on the landscape below.
Flak cannons fire a large amount of proximity-detonated ammunition at incoming torpedos and missiles. They excel at defending against these forms of weaponry, but they have very limited range. Operating them is as simple as inputting a new box of ammo into the rack on the wall.
Gauss guns fire 300mm Teflon coated tungsten rounds. Unlike other ship weaponry, these are not controlled by Bridge Staff using the tactical console and are typically manned by Munitions Technicians or available crew. Gauss guns require no maintenance. To man gauss guns, buckle yourself into the gauss gunner chair and you'll rise into the cockpit above. To fire, click on the overmap to fire a powerful short-range burst. Gauss guns eat through ammo quickly, and you'll ideally want someone below deck keeping you loaded at all times. Loading tungsten rounds is as simple as placing them in a crate, click-dragging it to the loading rack, and sending it up for reloading. Additional slugs can be acquired from a nearby Gauss ammunition dispenser that can be upgraded by science to produce slugs at a faster rate.
One thing that separates large ships from smaller ships is their ability to raise defensive shields to block projectiles and disrupt beam attacks. There are MAC rounds designed to disrupt shield patterns, and your ordnance tech can design even more effective solutions to this problem, but otherwise just keep shooting and don't give them time to recover, and you'll be the one salvaging their wreckage soon!
Once you've brought your enemy low, you can send over salvage teams to loot the enemy ship. If possible, find their cargo hold or vault and loot expensive stuff while you can; enemy ships may well be en route to confront you, so hurry your forces over to grab the loot and run! Remember that you can stack a battle pod high with goods, and look for rare items that aren't in normal supply aboard your ship. Some ships may have survivors, which may be very hostile towards you, so be careful!