*Minimal Spoilers*

If you're wondering what movie mindset you should be in for this game: Star Trek 2. This is a game where every individual shot can change the course of the battle. Instead of trading blows until your enemy is worn out, you should plan to fire all your weapons in one quick surgical strike that leaves your enemy crippled and helpless. To help with all the micromanagement this entails, you can pause the game with the spacebar and issue orders at any time.

The opening text is misleading. Your immediate goal is to reach the Federation fleet, but to win your goal is to take down the Rebel Flagship. At all times throughout this game you should be accumulating scrap and upgrading your ship to be able to take this dreadnought down.

Every system you want to try to explore as many beacons as possible to maximize the amount of scrap you pick up and new components you can buy. Every time you leave a beacon, the rebel fleet advances down the system from left to right. If you engage a rebel ship and it escapes, the rebel fleet will advance further this turn. If you jump to a beacon in a nebula (blue circle around the beacon) the fleet will advance slower. Don't exit the system until the rebel fleet prevents you from being able to explore any more beacons.

One thing the game doesn't let on about is that you can unlock a whole armada of different ships and variants to choose from. They could be considered different "classes" in the Fantasy RPG sense; the Kestrel could be considered a "Fighter," the Torus could be considered a "Mage," etc. You could install a drone system on a Kestrel, like you can teach a fighter spells in Diablo, but unless you have an oddball strategy in mind, it's better to use that scrap to capitalize on the Kestrel's weapons head start instead. Drones, cloaking devices, and boarding party transporters are best in the hands of specialists.

In the Kestrel, before you make your first jump, put one crewman in weapons, and one in engines. De-power your medbay and put that energy into the engines. This will give your ship a 20% chance to dodge any attack. NEVER leave the helm without a pilot or your evasion rate will drop to 0%.

An excellent tactic for the Kestrel in System 1 is to launch a missile at the enemy's shields, and once it connects, follow with a volley of burst lasers at their weapon systems. Then just keep firing burst lasers at their weapon systems until they surrender or blow up. The enemy will be unable to fight back and you will minimize the damage you take.

Don't spend any scrap in System 1 unless you come across a store selling items you seriously need in a Kestrel. Priority 1 is a weapon pre-ignition augmentation. Priority 2 is additional weapons, Priority 3 is a weapon recharge augmentation. If you don't find any of thse by the time you enter System 2, and there are no stores in the near vicinity, spend 90 scrap on 2 shield upgrades and 2 energy upgrades. Don't forget to transfer energy to your new shield layer! After this, if you can't find priority items, spend scrap on engine upgrades and energy upgrades to increase your evasion rate.

The best long-term strategy for the Kestrel is to get all 4 weapons slots filled and your weapon subsystem maxxed out in time for the Flagship. The ideal weapon loadout is an ion weapon (to hit the enemy bridge and knock their evade rate to 0%), a missile (to bypass shields and knock out a crucial system), a burst laser (to batter down their shields) and a beam weapon (for wreaking havok once their shields are down). Remember that the damage beams deal increases with every room the beam touches, so try to position your bean to pass through as many rooms as possible, there's no difference between sweeping down the center of a room and brushing the corner with one pixel.

Remember, you're outnumbered, but you're smarter than the enemy. Make use of that advantage!

i have to disagree on the point about transporters, drones and cloaking devices. these systems are very useful on all ships.
transporter can net you extra scrap from boarding ships instead of destroying them. also good at destroying the flagships weapons in the bossfight.
defensedrones protect you from missle and boarding drones (in the boss fight, too)
cloaking lets you dodge any nasty bursts from the enemy (especially in the bossfight)

My point isn't that these systems aren't useful, my point is that there are unlockable ships that specialize in these subsystems, and the Kestrel isn't one of them. Scrap is at an absolute premium in Normal mode and if the ship you're using has a head start in a certain area, you should maximize that advantage in time for the Flagship.

The Torus starts out with a Drone Control subsystem and a basic attack drone. For a Kestrel to catch up, you need to be lucky enough for the random number generator to spit out a Drone Control system, and spend hundreds of scrap buying that and some drone schematics just to reach the level the Torus starts at. Plus, when playing the Kestrel, if you're resigned to not using Drones, every drone schematic you pick up can be sold for an easy 25+ scrap for use in other areas.

On the other hand, the Torus only starts with a dinky ion cannon, and it would cost significantly more scrap to max out its weapon systems than the Kestrel's. So even though 4 active weapons are VERY useful, it's not wise to pursue that strategy on a drone specialist.

I'm not talking usefulness. I'm talking efficiency. I've edited the original post to hopefully make that point more clear.

Of course, Easy mode showers you in so much extra scrap that all bets are off, I suppose.

Drone control is sold at every second store, included is a free schematic which ist often Defense I, then you are safe from missiles and it costs only 80. I try to get it for every ship.