I have put a companion to my hand and then ult Karn Liberated.
What happens to the companion?
Karn Liberated and wished cards
From the CR:
Interestingly, the answer about what to do with Companions is still somewhat unclear. The rule above is mostly about Wished cards and Companions are outside the game to start so it makes sense they would follow the same rule. However, Commanders would still be put in the command zone (assuming they are not exiled under Karn) which suggests normal start of game procedures take effect. Essentially, this suggests that the Companion in the game would stay in the deck but that you could also choose another companion as part of the start of game procedures. The current Companion would affect the eligibility though. And in Commander you can't pick the same one so this may be more of a moot point anyway.
In any case, it looks like the answer for Companions is: if it is still outside the game, you can still declare it and use it as normal. If it was brought into the game, you leave it in the game and (maybe?) choose another Companion if you want if there is one that might still be eligible to be chosen. I am certainly open to discussion on the last part about choosing a new Companion but the rest seems clear enough.
727.2. All Magic cards involved in the game that was restarted when it ended, including phased-out permanents and nontraditional Magic cards, are involved in the new game, even if those cards were not originally involved in the restarted game. Ownership of cards in the new game doesn't change, regardless of their location when the new game begins.
Example: A player casts Living Wish, bringing a creature card into the game from outside the game. Then that game is restarted. The creature card will be part of that player's library when the new game begins.
Example: A player casts Living Wish, bringing a creature card into the game from outside the game. Then that game is restarted. The creature card will be part of that player's library when the new game begins.
Interestingly, the answer about what to do with Companions is still somewhat unclear. The rule above is mostly about Wished cards and Companions are outside the game to start so it makes sense they would follow the same rule. However, Commanders would still be put in the command zone (assuming they are not exiled under Karn) which suggests normal start of game procedures take effect. Essentially, this suggests that the Companion in the game would stay in the deck but that you could also choose another companion as part of the start of game procedures. The current Companion would affect the eligibility though. And in Commander you can't pick the same one so this may be more of a moot point anyway.
In any case, it looks like the answer for Companions is: if it is still outside the game, you can still declare it and use it as normal. If it was brought into the game, you leave it in the game and (maybe?) choose another Companion if you want if there is one that might still be eligible to be chosen. I am certainly open to discussion on the last part about choosing a new Companion but the rest seems clear enough.
