Cruise to catch up.....Allowed?

[sovereign]

Exactly. If a fighter decides to disengage from your capital via thruster, he is allowed to. But it counts as fleeing.

If you engage cruise however to chase after him, you count as fleeing as well.
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Simple as that. It gives fighters and bombers the mobility to escape a capital ship without dying. They still have to leave though, as they fled.

Wait, so if the fighter thrusts away and the cap goes into cruise, do they both have to leave system? Or is the second to flee allowed to stay in system (since he won... sort of) but just not re-engage?

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