FTL: Faster Than Light – Cloak Power Surge or Missiles in the Rebel Flagship Fight in FTL?

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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?

Best Answer

For phase 2:

During the power surge, the Flagship has 7 drones, randomly chosen from either 'Beam I' or 'Laser I' type. The beam drones do a tremendous amount of damage when your shields are breached. The 'attack drones' are very good at getting rid of shields, and will fire about 1.67 shots each during the 5-second drone surge.

The good news here is that the attack drones tend to fire a continuous barrage at your ship, so you will be able to 'see' your shields drop. Therefore, you can cloak as soon as your 'shield bars' drop to 1.

However, even if you do not have to cloak, you will have to leave your cloak available for the next surge.

The drones will fire an average of 6.8 shots over 5 seconds. I used a spreadsheet to estimate the damage taken, rounding off the amount of shots from 1.7/3.4/5.1/... to 2/3/5/7/9/10/12 and plugging that into a binomial, and assuming 5 damage is dealt by beam drones and the flagship beam artillery when shields are breached in addition to any regular damage. The drone surge is expected to deal far more damage than the missiles in all cases.

For phase 3:

This depends on your upgrades, and whether or not the 'laser' artillery happens to line up with the power surge.

Consult the table below. Use the '12' shot rows for when the laser artillery lines up. It lists the 'expected damage' you prevent by cloaking. You're expected to have at least 2 shields and at least 4 engines by now, so I have not included any smaller amounts. In any case with any less shields it's obvious you should always cloak the Power Surges.

There are a few cases where cloaking missiles works well. When the power surge does not line up with the laser artillery, and you have level 5+ engines with 4 shields or level 8 engines with 3 shields you should cloak the missiles and not the power surge. With a defense drone the requirement increases to 6 engines with 4 shields, as it reduces the missile damage by about a third. 

Engines  Shields  Dodge  Shots  Surge  Missiles  with DD       
      4        2   0.40      9   3.33      1.80     1.20
      5        2   0.45      9   2.93      1.65     1.10
      4        3   0.40      9   2.43      1.80     1.20
      5        3   0.45      9   2.01      1.65     1.10
      6        3   0.48      9   1.77      1.56     1.04
      7        3   0.51      9   1.53      1.47     0.98
      8        3   0.55      9   1.24      1.35     0.90
      5        4   0.45      9   1.18      1.65     1.10
      6        4   0.48      9   0.98      1.56     1.04
      7        4   0.51      9   0.81      1.47     0.98
      8        4   0.55      9   0.60      1.35     0.90
      8        3   0.45     12   2.75      1.65     1.10
      5        4   0.45     12   2.38      1.65     1.10
      6        4   0.48     12   2.15      1.56     1.04
      7        4   0.51     12   1.89      1.47     0.98
      8        4   0.55     12   1.54      1.35     0.90
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