Corrected entry: When Kirk and his crew stand before the Federation President, they are there to answer for the charges against them in the previous film. Other than trying to get a ship to Genesis, McCoy should not be included in the hearing since he had no way of knowing that Kirk would break him out of jail, steal the Enterprise, then escape to Genesis.
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Correction: Just like you said, they broke him out of jail. At that point he was a fugitive. And he went along with the plan, making him an accomplice.
Greenman37