Score

After defeating the Rebel Flagship, the player is shown stats for that game as well as their score. Score is determined with the following formula (rounded down to nearest integer):

Score = (s+10*b+20*d)*D

• s = scrap collected. Initial scrap (30 on easy, 10 on normal, 0 on hard) and scrap gained by selling at stores or additional gains from Scrap Recovery Arms does not count toward this total.
• b = beacons visited
• d = ships defeated by reducing hull or crew to zero
• D = difficulty modifier (1x Easy, 1.25x Normal, 1.5x Hard)

There are a few simple ways to increase score:

• Defeating ships rather than allowing them to surrender or escape will add 20 points on easy, 25 on normal and 30 on hard. It usually produces more scrap, too.
• A teleporter is a good investment since exterminating crew tends to yield more scrap than destroying the ship. 
• Do not get a Repair Arm.
• Following the longest path possible through each sector will not only increase the number of beacons visited but will give more opportunities for scrap and defeating ships.
• Visiting nebula beacons in non-nebula sectors will slow down the rebels (aprox. -47%) and allow the player to take a longer path. nebula beacons in nebula sectors will also slow down the rebels (aprox. -18%) but to a lesser degree.
• Certain events will delay the rebels, such as booby trapping a cache of weapons with missiles or letting a rebel ship live rather than scraping it after defeating another ship (scraping it doesn't count as defeating it, so letting them live to delay the rebel fleet only reduces the score by lost scrap). However, some events, like mercenaries, are too expensive to be worth it, as if you pay to delay the fleet you miss out on the scrap gained and defeating a ship.
• It is sometimes possible to fly through rebel controlled space for a while with good shields, a defense drone, and/or cloaking; even though no scrap will be gained, it will still pad the final score by increasing the beacon and ship counts.
• The Environmental Hazards in rebel-controlled beacons (frequent ion storms in nebulas and Anti-Ship Battery elsewhere) makes visting them a very risky way to gain a few extra points. 
• A ship that can take advantage of many blue options via a diverse crew, balanced upgrades, and useful weapons, drones, and augmentations will usually get more scrap. However, some blue options will merely result in avoiding a battle, resulting in a lower score.
• Playing on normal difficulty gives a 25% bonus, but because there is less scrap the score might end up lower, particularly if the player is forced to take shorter paths and avoid fights in the later sectors. Playing on hard difficulty gives a 50% bonus, but completing this mode is no small feat.

The game keeps records of the top four high scores for each ship layout, the top five high scores for all layouts, the difficulty played on, Advanced Edition Content enabled or not, and if the game ended in Victory. The game also records most ships defeated, most beacons visited in a run, most scrap collected, most crew hired, and the totals for these across all games. The names of crew members with the most repairs, combat kills, jumps survived, evasions piloted, and skills gained are also recorded.