Rick and Morty's season 5 finale "Rickmurai Jack" is another Citadel of Ricks episode, and one which explains the plot hole the Citadel creates in the first place. In the process of illustrating Evil Morty's plan, building over the course of the last several seasons, the writers manage to cover for one of the show's nagging contradictions: that Ricks are fundamentally opposed to the Citadel concept. It's in their nature to distrust government, so the fact they became a government themselves by organizing the Citadel runs diametrically opposed to their character. But the show has faced this conflict head-on, and with great success; some of the most beloved Rick and Morty episodes revolve around the Citadel.
The Citadel of Ricks was first introduced in season 1's penultimate episode "Close Rick-counters of the Rick Kind," where it's introduced to Morty as "a few thousand versions of me had the ingenious idea of banding together like a herd of cattle or a school of fish or those people who answer questions on yahoo answers." In the season 3 opener "The Rickshank Redemption," Rick destroyed the Citadel by transporting it into the Galactic Federation headquarters, causing mass destruction of bureaucracy. The Citadel is rebuilt and reshaped in the image of Evil Morty in season 3 episode 7 "The Ricklantis Mixup," better known as "Tales from the Citadel." Evil Morty's plan finally paid off in the most recent Citadel-centred episode, season 5 finale "Rickmurai Jack."
Evil Morty, plotting the Citadel's downfall since his season 1 debut at the end of "Close Rick-Counters of the Rick Kind," shows Morty the Citadel became a market for Mortys. Valuable for their ability to hide Ricks from their enemies - demonstrated via Evil Morty's control over "Evil Rick" in the first Citadel episode - the Citadel started manufacturing Mortys across thousands of timelines. They crafted the central finite curve from the infinite multiverse, pruning every timeline in which Rick isn't the smartest and most powerful, and growing more where he is. The collective value of the Morty market outweighs the repulsion of having to work together, resulting in that so-called herd of cattle, the Citadel.
Although Rick cites the Citadel's establishment as being the product of 'other' Ricks, while he has allegedly stayed clear of the place, Evil Morty reveals in "Rickmurai Jack" that C-137 was instrumental in the Citadel's development. By examining his memories, Morty discovers Rick's season 3 opener backstory wasn't a lie, that he rebuilt the Citadel with others who would become the council, and that upon his departure, he crashed home and returned to a Beth, hence kicking off the show's comedy format.
"Rickmurai Jack" covers a lot of ground; reuniting Rick and Morty after their "Forgetting Sarick Mortshall" breakup, telling Rick's backstory and that of the Citadel, and destroying the status quo as per Evil Morty's long-gestating plan. Where Rick and Morty goes from here is anyone's guess, but the writers tied up the lingering season 1 contradiction just before destroying the Citadel—a favorite move of theirs, apparently. One thing is for certain is that fans will await season 6 as eagerly as they did when season 2 left off on such a big cliffhanger.