Let $k$ be a perfect field of characteristic $p>0$ and let $\operatorname{W}$ be the ring of Witt vectors of $k$. In this article, we give a new proof of the Frobenius descent for convergent isocrystals on a variety over $k$ relative to $\operatorname{W}$. This proof allows us to deduce an analogue of the de Rham complexes comparison theorem of Berthelot [$\mathscr{D}$-modules arithmétiques. II. Descente par Frobenius, Mém. Soc. Math. Fr. (N.S.) 81 (2000)] without assuming a lifting of the Frobenius morphism. As an application, we prove a version of Berthelot’s conjecture on the preservation of convergent isocrystals under the higher direct image by a smooth proper morphism of $k$-varieties.

We complete our proof that given an overconvergent F-isocrystal on a variety over a field of positive characteristic, one can pull back along a suitable generically finite cover to obtain an isocrystal which extends, with logarithmic singularities and nilpotent residues, to some complete variety. We also establish an analogue for F-isocrystals overconvergent inside a partial compactification. By previous results, this reduces to solving a local problem in a neighborhood of a valuation of height 1 and residual transcendence degree zero. We do this by studying the variation of some numerical invariants attached to p-adic differential modules, analogous to the irregularity of a complex meromorphic connection. This allows for an induction on the transcendence defect of the valuation, i.e., the discrepancy between the dimension of the variety and the rational rank of the valuation.

In this paper, we define Swan conductors for unit-root overconvergent F-isocrystals using the theory of arithmetic 𝒟-modules due to Berthelot. Our Swan conductors are compared with the Swan conductors for ℓ-adic sheaves constructed by Kato and Saito using a geometric method. As an application, we prove the integrality of Swan conductors in the sense of Kato and Saito under the ‘resolution of singularities’ assumption.

We resolve the local semistable reduction problem for overconvergent F-isocrystals at monomial valuations (Abhyankar valuations of height 1 and residue transcendence degree zero). We first introduce a higher-dimensional analogue of the generic radius of convergence for a p-adic differential module, which obeys a convexity property. We then combine this convexity property with a form of the p-adic local monodromy theorem for so-called fake annuli.

Let $X$ be a smooth variety over a field $k$ of characteristic $p>0$, and let $\mathcal{E}$ be an overconvergent isocrystal on $X$. We establish a criterion for the existence of a ‘canonical logarithmic extension’ of $\mathcal{E}$ to a smooth compactification $\overline{X}$ of $X$ whose complement is a strict normal crossings divisor. We also obtain some related results, including a form of Zariski–Nagata purity for isocrystals.