Well, iirc the first time we meet Murdoc in the series is not their first encounter but him coming back for revenge beause MacGyver foiled something or other at some point in the past, and then thought Murdoc was dead. And that's pretty much the pattern set up. It doesn't make much of a difference if you only catch the fourth appearance or whatever, because he's still back for revenge. Or I guess sometimes MacGyver foiled yet another assassination plot, but it's very much a supervillain kind of setup where you can tune in at any point to their relationship.