A well-known conjecture states that for any [Formula: see text]-component link [Formula: see text] in [Formula: see text], the rank of the knot Floer homology of [Formula: see text] (over any field) is less than or equal to [Formula: see text] times the rank of the reduced Khovanov homology of [Formula: see text]. In this paper, we describe a framework that might be used to prove this conjecture. We construct a modified version of Khovanov homology for links with multiple basepoints and show that it mimics the behavior of knot Floer homology. We also introduce a new spectral sequence converging to knot Floer homology whose [Formula: see text] page is conjecturally isomorphic to our new version of Khovanov homology; this would prove that the conjecture stated above holds over the field [Formula: see text].