Given an involution on a rational homology 3-sphere Y with quotient the 3-sphere, we prove a formula for the Lefschetz number of the map induced by this involution in the reduced monopole Floer homology. This formula is motivated by a variant of Witten's conjecture relating the Donaldson and Seiberg--Witten invariants of 4-manifolds. A key ingredient is a skein-theoretic argument, making use of an exact triangle in monopole Floer homology, that computes the Lefschetz number in terms of the Murasugi signature of the branch set and the sum of Frøyshov invariants associated to spin structures on Y. We discuss various applications of our formula in gauge theory, knot theory, contact geometry, and 4-dimensional topology.

Let K be a knot in an integral homology 3-sphere Y, and Σ the corresponding n-fold cyclic branched cover. Assuming that Σ is a rational homology sphere (which is always the case when n is a prime power), we give a formula for the Lefschetz number of the action that the covering translation induces on the reduced monopole homology of Σ. The proof relies on a careful analysis of the Seiberg--Witten equations on 3-orbifolds and of various η-invariants. We give several applications of our formula: (1) we calculate the Seiberg--Witten and Furuta--Ohta invariants for the mapping tori of all semi-free actions of Z/n on integral homology 3-spheres; (2) we give a novel obstruction (in terms of the Jones polynomial) for the branched cover of a knot in S3 being an L-space; (3) we give a new set of knot concordance invariants in terms of the monopole Lefschetz numbers of covering translations on the branched covers.

Let Y be a closed and oriented 3-manifold. We define different versions of unfolded Seiberg-Witten Floer spectra for Y. These invariants generalize Manolescu's Seiberg-Witten Floer spectrum for rational homology 3-spheres. We also compute some examples when Y is a Seifert space.

We use the construction of unfolded Seiberg-Witten Floer spectra of general 3-manifolds defined in our previous paper to extend the notion of relative Bauer-Furuta invariants to general 4-manifolds with boundary. One of the main purposes of this paper is to give a detailed proof of the gluing theorem for the relative invariants.

Kronheimer-Mrowka recently proved that the Dehn twist along a 3-sphere in the neck of K3#K3 is not smoothly isotopic to the identity. This provides a new example of self-diffeomorphisms on 4-manifolds that are isotopic to the identity in the topological category but not smoothly so. (The first such examples were given by Ruberman.) In this paper, we use the Pin(2)-equivariant Bauer-Furuta invariant to show that this Dehn twist is not smoothly isotopic to the identity even after a single stabilization (connected summing with the identity map on S2×S2). This gives the first example of exotic phenomena on simply connected smooth 4-manifolds that do not disappear after a single stabilization.