Metal Gear Solid Delta: Snake Eater Bosses: The Boss

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You can only counter CQC the boss if no weapon is in your hand / a weapon that allows you to use CQC.
For the CQC to counter, you need to wait for the slowdown to happen, then press the CQC button.
for turn 1 and 2 of the CQC cutscene, you only need to counter her once. On turn 3 onwards you need to counter her CQC 2 times.

You can counter the boss before she first connects with you as found by Pythonicus:

SVD lets you shoot the Boss only once, then the health bar locks up (iframes).

EZ Gun takes 4 cycles of 3 shots each after her being slammed on the ground.
Mosing Nagat takes 3 cycles of 3 shots each after her being slammed on the ground.

A fast strat utilizing the Cig Spray - unfortunately only viable on Glitchless/All Bosses when the Lab and Fear are not being skipped due to the location of the Cig Spray being only available in the Granini Gorki Lab.
by Kemist

Pazzo found this strat on Normal using 2 body shots with the Mosin then a Stun. Repeat multiple times
“ you need to throw the last stun right when she's going up, and the last 2 shots have to be extremely fast”