Boss + Continue!

[Hector]

I see a lot of people talking about wanting to skip the boss fight and continue.

I think the answer is to allow BOTH.

If you beat the boss fight you get a free repair and then the Federation asks you to go on a second mission: Flagship is destroyed, rebels are retreating, but NOT out of the fight. Federation needs your crew to mop up the problem, plus restore order across the sectors.

Now, some icing on the cake would be if you agree to the mission all crew currently on board get 3 star rank and equivalent bonus in cooldown shortening, ship gains 10 additional hull, 4-6 extra power bars (need to purchase) plus 2 extra expansion bar in all systems (need to purchase)

Give some message about 'retrofitting' the ship.

[Milkshake]

Really, really, really like the idea.

I also like the fact that there can be even harder enemies after the boss, because with the extra system power and hull, you should be able to get enemy ships with for example 5 shields.

Alternately you could also try and work your way back to sector 1 to like you said: Mop op the enemies still left behind.
You could make a sort of second boss in sector 1: "The Rebels' Final Stand" if you will.

Anyway like the idea of being able to continue after defeating the boss and the even higher upgrades and tougher enemies:D

[Mr.Mafia]

Maybe, as you continue on, every beacon you visit will be in rebel territory, and as you continue on the rebel territory will shrink. Or maybe a requirement of beacons you have to clear in order to continue on to the next sector.