A graph $G$ is $H$-free if it does not contain an induced subgraph isomorphic to $H$. The study of the typical structure of $H$-free graphs was initiated by Erdős, Kleitman and Rothschild, who have shown that almost all $C_3$-free graphs are bipartite. Since then the typical structure of $H$-free graphs has been determined for several families of graphs $H$, including complete graphs, trees and cycles. Recently, Reed and Scott proposed a conjectural description of the typical structure of $H$-free graphs for all graphs $H$, which extends all previously known results in the area. We construct an infinite family of graphs for which the Reed-Scott conjecture fails, and use the methods we developed in the prequel paper to describe the typical structure of $H$-free graphs for graphs $H$ in this family. Using similar techniques, we construct an infinite family of graphs $H$ for which the maximum size of a homogenous set in a typical $H$-free graph is sublinear in the number of vertices, answering a question of Loebl et al. and Kang et al.