We study global aspects of the mean curvature flow of non-separating hypersurfaces $S$ in closed manifolds. For instance, if $S$ has non-vanishing mean curvature, we show its level set flow converges smoothly towards an embedded minimal hypersurface $Gamma$. We prove a similar result for the flow with surgery in dimension 2. As an application we show the existence of monotone incompressible isotopies in manifolds with negative curvature. Combining this result with min-max theory, we show that quasi-Fuchsian and hyperbolic $3$-manifolds fibered over $mathrm{S}^1$ admit smooth entire foliations whose leaves are either minimal or have non-vanishing mean curvature. We also conclude the existence of outermost minimal surfaces for quasi-Fuchsian ends and study their continuity with respect to variations of the quasi-Fuchsian metric.