Nikara, Lair Scavenger

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.

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.

"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 a creature with counters on it leaves the battlefield at the same time as Nikara, Nikara's ability triggers for that creature.

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.

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.