In Commander, the command zone replacement effect is optional. When your commander would go to the graveyard (or exile), you may choose to redirect it to the command zone instead — but this choice happens at the moment the card would move there (CR 903.9). If you choose not to use the replacement effect, or if you simply don't act in time, the commander ends up in the graveyard as a normal card.
Once your commander is sitting in the graveyard, it is just a card in the graveyard. Opponents can interact with it using any card that targets or affects graveyard cards — including Bojuka Bog, which exiles all cards in a target player's graveyard when it enters the battlefield (CR 609.3, 800.4g).
Importantly, the command-zone replacement effect (CR 903.9) only triggers at the moment the commander would move to a zone, not retroactively after it is already there. So once it has settled in the graveyard, there is no second chance to redirect it to the command zone before Bojuka Bog resolves.
Example: Your Atraxa, Praetors' Voice is destroyed and you let it go to the graveyard instead of moving it to the command zone. Your opponent then plays Bojuka Bog targeting you. Atraxa is exiled — it does not get to go to the command zone because it is being exiled from the graveyard, not from the battlefield.
The lesson: if you want to protect your commander from graveyard hate like Bojuka Bog, always use the replacement effect to send it to the command zone when it would first move there.
Unofficial fan resource — not affiliated with or endorsed by Wizards of the Coast. Answers are AI-generated estimates grounded in the Comprehensive Rules and are not a substitute for an official judge. Verify anything match-critical.