Much of Super Mario RPG's gameplay is outside monster battles and plays like an isometric 3D platformer, in which traditional Mario elements such as punching floating question blocks from below are prominent. There are no random encounters and as such enemies are visible in the field; a battle ensues only if Mario comes in contact with one.
This allows the player to evade unnecessary battles. Ultimately, the player will gain a party of five characters, though only three members can be used during a battle at any given time. Mario is always in the player's party, but the other two characters can be selected before battles. Each of the five characters has a unique set of attacks and techniques.
For example, Princess Toadstool's abilities are primarily healing techniques, whereas Geno and Bowser have offensive attacks that deal high amounts of damage. The combat is based on a traditional turn based battle system with the addition of action commands that amplify a move's effects.
The player starts each turn by choosing to attack, defend, run, use an item, or perform magic from the combat menu. Each region has distinct characteristics held by its inhabitants; Mushroom Kingdom is inhabited by Toads , Moleville is inhabited by moles, Monstro Town is populated by reformed monsters, Yo'ster Isle is where Yoshi and his eponymous species reside, and Nimbus Land is an area inhabited by cloud people.
Bowser's Castle is another prominent location in the game, as it holds the portal to the main antagonist's home world.
As in most Mario series games, the main protagonist is Mario, whose initial goal is to rescue Princess Peach Toadstool from Bowser.
However, the story takes on an unusual and very important twist. Soon after the start of his journey, the Smithy Gang invades the world. While attempting to stop the group, Mario is joined by Mallow, a cloud boy who thinks he is a tadpole; Geno, a doll possessed by a celestial spirit from the Star Road; Bowser, whose armies have deserted him out of fear of the Smithy Gang; and Princess Toadstool, who was lost in the turmoil that occurred when the Smithy Gang arrived. The Smithy Gang is led by Smithy, a robotic blacksmith from an alternate dimension with aspirations of world domination.
Mario lands back at his pad and meets up with Toad, who tells him he has to rescue Toadstool. Mario returns to Bowser's castle, but Exor destroys the bridge, preventing him from entering.
Mario and Mallow enter the castle to defeat gang boss Mack,  and subsequently find a mysterious Star Piece. Mallow accompanies Mario to Tadpole Pond so they can get advice from Frogfucious, Mallow's grandfather. He reveals that Mallow isn't really a tadpole, and says Mallow should join Mario on a quest to find the seven Star Pieces as well as Mallow's real parents. The duo travel to Rose Town where they meet a star spirit who has taken control of a doll named Geno.
After battling the bow-like creature Bowyer, who is immobilizing residents of Rose Town with his arrows, they retrieve another Star Piece. Geno joins Mario and tells him the Star Piece is a part of the shattered Star Road, where he normally resides.
Geno has been tasked with repairing Star Road and defeating Smithy, so that the world's wishes may again be heard. They join forces to fight a common enemy, as Bowser wishes to reclaim his castle. The new team intercepts Princess Toadstool just before she is forcibly married to Booster, but it turns out that the wedding wasn't real and that Booster only wanted the wedding cake. A statue maker informs them that Valentina has the rulers of Nimbus Land being held captive, and her sidekick Dodo is impersonating the prince.
Dodo would make Valentina his queen. The statue maker recognizes Mallow as the true prince, then disguises Mario as a statue to infiltrate the castle. There they defeat Valentina and Dodo. The newly liberated king and queen, Mallow's parents, inform the group that they saw a star fall into the nearby volcano. After traveling to Barrel Volcano to obtain the 6th Star Piece, Mario's party learns that the final piece must be held by Smithy in Bowser's castle. The collected Star Pieces are used to repair the Star Road, Geno returns to the Star Road, Bowser rebuilds his castle with his newly reformed army, Mallow regains his rightful title as prince of Nimbus Land, and Mario and Princess Toadstool return to the Mushroom Kingdom to celebrate their victory.
There have been calls from all ages, and from young girls, for another character to which they could become attached. Mario was the best, but had not been in an RPG.
Miyamoto also wanted to do an RPG using Mario. There happened to be a chance for both companies to talk, which went well. Miyamoto led teams at Nintendo and Square, who spent over a year developing the graphics. The developers created the interior elements such as columns, stairways, and exterior elements with advanced computer modeling techniques.
Special lighting effects were used to create shadows and reflections that were meant to improve the 3D elements. Square's Final Fantasy series was the model for the battle sequences, while the tradition of Super Mario Bros.
Mario's ability to jog in eight directions and jump up or down in three—quarter perspective gave him a comparatively large range of motion. A Link to the Past. The battle screens, using pre-rendered sprites as in the rest of the game, included attack animations of equipped weapons. Compared with standard SNES games, the additional microprocessor allows higher clock speeds ; faster access to the random-access memory RAM ; greater memory mapping capabilities, data storage, and compression; new direct memory access DMA modes, such as bitmap to bit plane transfer; and built-in CIC lockout for piracy protection and regional marketing control.
Shimomura regards the Super Mario RPG soundtrack as one of the turning points in her career as a composer. The two-disc set contains 61 of the game's 73 songs.