"Partner with [name]" represents two abilities. The first is a triggered ability: "When this permanent enters the battlefield, target player may search their library for a card named [name], reveal it, put it into their hand, then shuffle their library."
If your Commander deck has two commanders, you can only include cards whose own color identities are also found in your commanders' combined color identities. If Haldan and Pako are your commanders, your deck may contain cards with blue, red, and/or green in their color identity, but not cards with white or black.
A creature with a "partner with" ability can't partner with any creature other than its designated partner. Losing a partner ability during the game doesn't cause either to cease to be your commander.
Magic: The Gathering · ™ & © Wizards of the Coast · Illus. Grzegorz Rutkowski
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The second ability represented by the "partner with [name]" keyword modifies the rules for deck construction in the Commander variant and has no function outside of that variant. If a legendary creature card with "partner with [name]" is designated as your commander, the named legendary creature card can also be designated as your commander.
If a creature with counters on it leaves the battlefield at the same time as Nikara, Nikara's ability triggers for that creature.
If a creature with +1/+1 counters on it receives an equal number of -1/-1 counters and this causes it to be destroyed by lethal damage or put into its owner's graveyard for having 0 or less toughness, Nikara's last ability triggers. That's because the ability checks the creature as it last existed on the battlefield, and it still had those counters on it at that point.
Once the game begins, your two commanders are tracked separately. If you cast one, you won't have to pay an additional {2} the first time you cast the other. A player loses the game after having been dealt 21 damage from one of them, not from both of them combined. Command Beacon's effect puts one into your hand from the command zone, not both.
Note that the target player searches their library (which may be affected by effects such as that of Stranglehold) and that the card they find is revealed, even though these words aren't included in the ability's reminder text.
Both commanders start in the command zone, and the remaining 98 cards of your deck are shuffled to become your library.
The triggered ability of the "partner with" keyword still triggers in a Commander game. If your other commander has somehow ended up in your library, you can find it. You can also target another player who might have that card in their library.
Nikara's last ability causes you to draw only one card and lose only 1 life, no matter how many counters or kinds of counters that creature had on it.
