Most versions of Puyo Puyo~n remove the Sun Puyo gimmick from its predecessor. In its place is the "Super Attack" mechanic, where characters gain SP by making chains and, when they have enough, can unlock a character-specific ability by sacrificing their current pair of Puyos. The single player mode of the Dreamcast version features a singular gauntlet, with each stage having unique field gimmicks and the story scenes more closely resembling a visual novel than in previous games. The game in general moves much slower than previous games, between the drop speed, Super Attacks, and aforementioned field gimmicks.
Though Sega owned the Puyo Puyo series at this point, the deal that Compile made with Sega allowed Compile to continue to use the series as they saw fit; as a result, the game was ported to consoles that Sega was directly competing against at the time (and while this was nothing new for the series or even some of Sega's other series, this particular instance resulted in the company's own name, "Sega Enterprises, Ltd", to be listed on the competitor's hardware via the game's title screen and end credits). The PlayStation and Nintendo 64 versions are similar to the Dreamcast version aside from each having a unique gameplay mode and other quirks, while the Game Boy Color port is a radically different game built on the engine of Pocket Puyo Puyo Sun that features Sun Puyos, different Super Attacks, playable characters not included in the console versions, and a different story beyond the base premise.
The Dark Prince has started a circus, which Arle Nadja and Carbuncle decide to attend. For one of his magic tricks, he makes Carbuncle disappear. While entertaining at first, the show concludes with Carbuncle still nowhere to be found. Thus, Arle conducts a search for him, battling familiar opponents along the way.
Tropes present in Puyo Puyo~n:
- All Just a Dream: Arle's search for Carbuncle in Pocket Puyo Puyo~n turned out to be a daydream. He was returned to her completely fine at the ending.
- Art-Shifted Sequel: Yon, for the most part, trades in the Super-Deformed style of its predecessors for more traditional anime-styled art. Pocket adverts this, keeping the same chibi-esque designs as previous entries.
- The Artifact:
- Sun Puyo were retained in Pocket Puyo Puyo~n despite the plot having nothing to do with the sun.
- Much like Rulue in Puyo Puyo (1992), Minotauros doesn't have voice acting in Pocket Puyo Puyo~n because he wasn't playable in Sun or console Yon where the rest of the voice acting is pulled from.
- Circus of Magic: A visit to the Puyo Puyo Circus headed by the Dark Prince kicks off the plot.
- Comeback Mechanic: Most of the Super Attacks in console versions are defensive in nature, made obvious when the CPU repeatedly uses its Super Attack as it nears defeat.
- Console Cameo: The SEGA Dreamcast's iconic orange swirl appears in the Nuisance Puyo cache at a high enough amount in Yo~n. Strangely this would be kept in the later Playstation and Nintendo 64 versions.
- Darker and Edgier: Downplayed. This game adapts a different art style with a more subdued color palette and realistic designs, and takes a small step back from the comedy for a slightly more serious story similar to Madou Monogatari games.
- Divergent Character Evolution: This is the first game in the series that attempts to give each character their own gameplay characteristics; previously, the choice only mattered for aesthetics.
- Easter Egg: Attempting to put the game into a CD player will have Arle freak out, alerting you to not put the game in a CD player.
- Fake Longevity: The game's main single-player mode takes way longer to complete than any of its arcade-based predecessors. It doesn't get there by way of additional content, however; it takes longer because many of the game's unique quirks are designed to slow the game down. The Game Boy Color "port" ditches almost all of said quirks in favor of a single player mode where nearly half of the opponents are optional.
- Gameplay and Story Integration: Carbuncle doesn't appear on the playfield at all, while all other games have an area set aside for Carbuncle to play around in. Subverted in the original Dreamcast release, where Carbuncle DOES appear... on the VMU's screen!
- Hoist by Their Own Petard: The final boss in Yo~n, Doppelganger Arle. They did not have to put the blocks to summon a million garbage blocks on both sides!
- It's All Upstairs From Here: Inverted in the console versions' final stage. The player has to dig their way through high-health Hard Puyo in order to reach one of two 500k Point Puyo, which generates enough nuisance to bury the opponent dozens of times over.
- Later-Installment Weirdness: This game, being Compile's final mainline game, has an Art Shift, Tone Shift, Limit Breaks, and a final boss who isn't Dark Prince.
- Meta Twist: Dark Prince is not the final boss for the first time in the series. The antagonist is instead Doppelganger Arle.
- Reformulated Game: Pocket Puyo Puyo~n is a much more loose port of Puyo Puyo~n than its Game Boy predecessors are to their respective arcade games; in an twist, it does so by being a Mission-Pack Sequel to Pocket Puyo Puyo Sun (down to utilizing Sun's entire soundtrack) instead of directly copying the changes of its Dreamcast big brother. The game has an almost completely different set of Super Attacks that, unlike the console game, are not character-locked. The cutscenes are different, there are no field gimmicks in story mode, and the player is given limited control of the number of opponents that they face. Most prominently, the game utilizes Sun Puyo by default, though the player is given the option of disabling them.
- Rocket-Tag Gameplay: You can easily squish Doppelganger Arle via snatching the 500k Point Puyo on your side first, and vice versa.
- Victor Gains Loser's Powers: Unlike the console versions, where Arle can only borrow a Super Attack from one of her "party members" (Draco, Serilly, Witch, Chico), Pocket Puyo Puyo~n lets her obtain any character's power by defeating them.
