Note: This is completely focused on the normal partner mechanic. But I will still look at Partner with or Backgrounds and what can be done with these.
Under normal circumstances, most decks will have only one commander. There are, however, ways to have multiple commanders. With the Set Commander Legends the Partner mechanic was introduced. Later on in one of the Dungeon and Dragons sets the Background mechanic followed. Both of these allow for a pair of cards to be in the command zone, but they reduce the size of the remaining deck to 98. A deck no matter the commander count should have only 100 cards in total after all. This changes some maths of what you want to have in the deck but also gives more flexibility since there are potentially two effects in the command zone readily available. In the best case they synergize, sometimes they are only there to give certain colors.
In fact, partner commanders are one of the few ways to have variety in 4 color commander decks besides a very few selected legendary creatures (number growing). Due to the inherent strength of always having 1 card more available, partner commanders are also often used in competitive commander or cEDH.
In every case, the combined color-identity of each card that is a commander defines the whole color-identity of the deck.
Partner Mechanic
The original partners were cards printed in the Commander 2016 expansion. This set was a bunch of 100-card pre-made decks that contained in total 15 cards with the partner mechanic. All of these were dual-colored cards, thus allowing three- or four color decks at this point in time, but no single-color decks. Notably, this included some player-wanted prints of characters that never before had a unique card.
The mechanic itself is very easy:
In your 100 cards commander deck you can have two legendary creatures as your commander if both have the same partner mechanic. Thus, the command zone stretches to two commander cards, and the other 99 shrinks to 98 cards in your main deck [5]. A definitive disadvantage against Mill decks.
Given the original 15, there are 105 possible combinations:
C(15, 2) = 15! / (2! (15 - 2)!) = 105
The original cards have all 10 Ravnica guilds represented but some of them got duplicate cards for the color combinations. Boros (WR), Golgari (GB), Izzet (UB), Orzoh (BW) and Simic (GU) got duplicated cards. These are all enemy color pairs. The other guilds only got one cards each. This means from this 15 cards set, you can only make 5 distinct two-colored decks, all three-color deck variations, although some have more commander-choices here, and all 5 four-color deck variants, again with some having a slightly bigger card selection for the commanders. Being able to build four colors decks was actually one of the goals of the partner mechanic. [6] Currently I do not know why that choice was made, except that Wizards wanted to push the enemy color commander choice. [9]
This in itself was a very powerful effect. In Magic card advantage wins games, and essentially doubles the cards that are always available in the commander zone. It also helps that many of these new legendaries were rather powerful.
Flavoring-wise, the commanders were often from different planes, although some of them could be from the same plane. There is no binding contract what partners could go together; in theory, allowing endless combinations, in practice, making players gravitate towards the most powerful combinations. A variant of this was later explored, called “Partner with”, that only allowed certain cards to be partnered together, thus more heavily restricting deck-building. In general, cards that have the “pure” partner mechanic are only printed rarely these days. This is due to its inherent power. Mark Rosewater put the Partner Mechanic on a 10 in the storm scale, a rough measure of whether a mechanic is too powerful to randomly be printed into sets. [7]
Thus, there are only a few more appearances of cards with the pure partner mechanic,
First, in 2020 the Commander Legends was printed. This set included reprints of the original 15 partner cards and 41 new, mono-colored cards at different rarity. This now meant it was possible to have mono-colored partner decks, easier to have two-color decks, but one still needed the original 15 cards to have a four-colored partner deck. This alone more than doubled the choice of available commanders at the time, [8] There were 1037 “solo”-commanders, the 56 partner-cards allowed 1540 possible combinations! So in total, we suddenly had 2577 possible commander decks. Reception to this was, of course, mixed from what I saw of the original reddit posts.
In total, there were 30 new partners printed at Uncommon, 5 at rare and 5 at mythic, and one designated as a special rarity, the Prismatic Piper.
The only single partner cards, printed in a set was [[Yoshimaru, Ever Faithful]] in Neon Dynasty Commander in 2022. It was possible to get this card in set-booster or collector-booster and it is the only single-partner add-on that Wizards ever did. Just for flavor-reasons of building around a “good boy” the card is very popular.
The next set to introduce more partners to Magic, was Unfinity in 2022. These Partners notably were all unset - or Acorn cards. That means they were technically not legal in any format, but could be used in a deck with an appropriate pre-game discussion. These were in total 5 new mono-colored partners all printed at rare. Thus the available color-combinations do not change, but with 62 partner cards we now 1891 possible combinations. (if you allow these unset decks in your pod)
C(62, 2) = (62 × 61) / 2 = 1891
Then, the last set to introduce a new single partner card was Ixalan Commander. This is the card [[Francisco, Fowl Marauder]], a mono-black pirate from the pirate pre-constructed deck. He pushes the amount of partner cards to 63, and thus 1953 possible partner combinations. Almost two thousand.
Recently, Wizards have taken to reprint the partner cards, especially the stronger ones, but often give them universes beyond flavor. This means the partner cards are technically still in sets for commander-players, but they do not add new partner cards. This is either for balance reasons, but I think more likely they are holding off to print more general partners cards until they can use them to sell a set. This could be next year in 2027, most likely as a single inclusion, or over the following years with more dedicated commander sets.