What it does
I'm not aware of "Command Protocols" as an official Magic: The Gathering keyword or ability. It doesn't correspond to any printed mechanic I can verify, and I don't want to invent rules text that could mislead your gameplay.
It's possible you're thinking of something with a similar name, or a fan-made/custom card mechanic. A few real abilities that might be what you mean: "Protocol" isn't standard either, but there are mechanics like Domain, Commander tax, or device/contraption-style abilities from Unstable.
If you can tell me the exact card or set you saw it on, I can give you a precise, accurate explanation of how it works and how it matters in Commander. I'd rather confirm the real mechanic than guess at rules nuances that could cost you a game.
Iconic cards with Command Protocols
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