Cloak the power surge or the missiles in the Rebel Flagship fight?
When fighting the "Rebel Flagship" in FTL, you can use cloaking to dodge either the Missiles or the Power surge. With level 2 cloaking, you can dodge both of these for the first volley if timed right. However, afterwards they will de-synchronize, as the power surge will charge up during your cloak, while the missile artillery will not.
Hence sometimes, especially with less powerful weapon loadouts, you will have to choose to dodge either a Power Surge or the Missiles. Which is the smarter choice?
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How do you beat the Rebel flagship in FTL?
With hacking, cloaking, and a teleporter: hack and cloak missiles, while boarding the ion and beam weapons. This neutralises the Flagship's offence. You can then board missiles and gradually kill off the enemy crew, who will have difficulty escaping to the medbay since hacking locks the doors.FTL Guide: How to Kill Rebel Flagship Final Boss
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Images: inna mykytas, inna mykytas, Jakayla Toney, inna mykytas