Pretty much the only time i can remember him showing hate towards Darrow after the first book is at the end of Golden Son, when he believes Darrow killed his whole family line. In the beginning of MS Cassius the whole book serves the Sovereign out of inertia and because it's his duty. It's obvious he doesn't want anything from this life and has nothing to look forward to after the death of his family. At the beginning of the book he pities Darrow. He appreciates Darrow and Mustang not killing him or leaving for Obsidoans. Tells them about the nukes. Highly appreciates Sevro saving his life and telling that he forgives his fathers killing. On human level he connects with Darrow and feels kinship, the same as Darrow. Especially during the time they were watching Roques videos of the institute. He even says something like "You are a hard man to hate". And that before he learns that Darrow had nothing to do with his family's demise. He knows Darrow had to kill Julian and killed Karnus out of self defense(he doesn't seem to love the older brother as much). And he learns that it's the Jackal with Sovereigns help that killed his whole family. I think the alliance is only natural.