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Given a link in the 3‐sphere, Ozsváth and Szabó showed that there is a spectral sequence starting at the Khovanov homology of the link and converging to the Heegaard Floer homology of its branched double cover. The aim of this paper is to explicitly calculate this spectral sequence in terms of bordered Floer homology. There are two primary ingredients in this computation: an explicit calculation of bimodules associated to Dehn twists, and a general pairing theorem for polygons. The previous part (Lipshitz, Ozsváth and Thurston ‘Bordered Floer homology and the spectral sequence of a branched double cover I’,  J. Topol . 7 (2014) 1155–1199) focuses on computing the bimodules; this part focuses on the pairing theorem for polygons, in order to prove that the spectral sequence constructed in the previous part agrees with the one constructed by Ozsváth and Szabó.

Bordered Floer homology and the spectral sequence of a branched double cover II: the spectral sequences agree