It was a case where nothing was as it seemed: two seemingly-identical dead men, killed in revenge for the death of a frat pledge a decade earlier. But neither of them was the actual murderer. And the guy who killed them, he didn't assault the guy who designed the doppelganger software. That was the original murderer. I think.
Then there was a third lookalike, who refused to have anything to do with things...
The A-storyline in Elementary Season 4 Episode 3 felt sort of muddled and confused, though I imagine that was how Sean Cudlow felt when he was confronted with the second doppelganger. Too bad for Sean, he didn't even kill the right people. So much for revenge.