It's actually 4D chess. Malzel uses a chess piece for his emblem because the game writes him as a calculating strategist like Lelouch from Code Geass. That's evidenced throughout the game:>He's literally ORCA's strategist>His dialogue is peppered with "pawn" and taking people of their "leashes">He's manipulative (see Hari and Strayed in the League path)>His emblem is a chess piece>His NEXT's name is "Opening">Both Neo Nidus and Thermidor leave him in charge of winning the war effort even they themselves would lose the individual battles.
Everything about him is used to emphasize that he's in charge of ORCA's strategies. He's supposed to be this cunning mastermind.
And that's why it's ironic how he doesn't even know that he's being played at all. ORCA was supposed to be in cahoots with Omer, but what Malzel didn't know is that they never had any real intention of completing the Closed Plan. Malzel had absolutely no idea that he was being played like a damn fiddle by Omer and Thermidor.
You can see Malzel's true loyalty the moment he dies:>This... is my time... No matter. I'm of no use anymore... for mankind's golden age...
The golden age he speaks about is supposed to be the day mankind was liberated from the Assault Cells. It's the same idea mentioned by Neo Nidus if he fails to protect the Ehrenberg cannons. Unfortunately for them, the game was rigged from the start. For all Malzel's scheming, he was just a pawn.