Murdoch suspects James Pendrick of crimes on a regular basis, while still applauding his inventions. In one of the best season openers, they fly a plane together.
When Pendrick moves on to producing movies, he bases the first picture-with-a-story on Murdoch (the first motion pictures were, as Murdoch Mysteries correctly show, series of moving images: trains, carriages, shoot-outs).
I wouldn't be surprised if, like Kirk and Spock, Murdoch-Pendrick were "shipped"--Pendoch? Murdrick? In a later episode, Pendrick--who is continually betrayed by his assistants--wonders if he could "change his nature" to get together with the one male assistant who defended him.
He sadly decides, "No." And he is standing next to Murdoch when he comes to that decision.