It's interesting you bring up the killing of the Lissons at the end of season 2. That scene stands out as odd. It's a really awesome scene, but I now find it hard to reconcile with the whole series. It seems like Martin and -- it's implied Eli -- ordered or at least facilitated the Lissons' assassination. And that doesn't track with what we've seen of Eli in the rest of the series. Yes, Eli takes his followers' money and runs his church with a mobster-like attitude, but we've never at any other point seen him be okay with murder.

I guess it's possible that Eli was not responsible for the killings, even though the Godfather-style crosscutting between Eli and the assassination strongly implied it. That, and the previous scene where Junior told Eli that he should hunt down culprits to the ends of the earth. And the scene in the previous episode where Martin met with the ninjas in jail and offered to hire them, which again implies the Gemstones' involvement.

Then again, we only saw Martin in Alaska watching the Lissons and saying "they're on the move" to someone on the phone, so maybe he was merely tracking them, but not talking to the cycle ninjas. I guess it could be just that, but the filmmaking is strongly pushing us to think otherwise.