The game's storyline starts out when Mario is invited to Moonview City by famed Chronologist, Professor Koopenstein to test out his newest invention: A Time Machine. After a successful trial run, all the stars on the Moonview City Clock-Tower fade to gray and all the clocks in the Mushroom Kingdom turn to the 12 o'clock position and start counting backwards. After an investigation, this is due to the scattering of the Chrome Stars, which keep the world's time flowing by powering up the Grande Star Clock. However, the Chrome Stars are scattered not only geographically, but also in different periods of time. As such, Mario must recover the Chrome Stars across time to stop the time of the Mushroom World from stopping to a standstill. Like all Paper Mario games, there are eight chapters, but after the final boss there are 4 extra Chapters to explore for the after-game plot.
Information on the game's characters, enemies items and plot can be found in here.
This story has examples examples of:
- Adult Fear: Zarge and the other Crescent Shade villagers get distressed once Xarrie & Yarrie get lost in the woods.
- Battle Theme Music: There's a different remix of the battle theme for every Chapter's Location, as well as having different themes for every boss.
- Call-Back: There are many references to the first 3 Paper Mario games.
- Colour Coded Stones: The Chrome Stars which go in hue order (red, orange, yellow, green, teal, cyan, blue, violet, pink) and then in bronze, silver and gold.
- The Fashionista: Goombeverly: Her outfit changes depending on the location of the Chapter.
- Great Big Book of Everything: Literally. Goombeverly's Tattle Log not only includes entries on enemies, but also locations, NPC's and recipes.
- No Hero Discount: Mario is charged for everything even in places which he has saved. Subverted in Chapter 6, where when he first arrives everything is double price, but once saving the town everything is free.
- Pass the Popcorn: All battles have an audience spectating which change their attire appropriately according to the time period the battle is set in.
- Previous Player-Character Cameo: All of Mario's partners from the first two games reappear occasionally in Moonview City.
- Product Placement: Mario's Mailbox V3 looks like a 3DS
- Punny Name: Most of the Toad characters, like aspiring painter Arh T. or the chef Suee T.
- Ragtag Bunch of Misfits: Among your party members you have a Valley Girl Fashion Victim, a smug business tycoon who used to be a painting, a condescending and quick-tempered knight turtle, an absent minded sheriff, an over-exaggerating Pharaoh that explodes, an overly optimistic mountaineer, a Ukrainian secret agent dog who was supposed to assassinate you, a cowardly prankster Sergeant that freezes anything in contact with him, a hyperactive artist, and maybe a shadow-creature that tirelessly works with flowers all day, a lady's man saxophonist dinosaur and/or a robotic marvel in the form of a dog.
- Suspiciously Similar Substitute: Some of Mario's partners are functionally similar or identical to previous partner's abilities, like Goombeverly to Goombella & Goombario, Koopert to Koops & Kooper, Dr. Booston to Bow, and Tutankaboom to Bombette & Bobbery.
- Time Abyss: The Tribe of Time has been weaving the fabric of time since they started creating Time itself.
- Time Stands Still: What happens to the Mushroom World if the Chrome Stars aren't recovered in time.
- Valley Girl: Goombeverly, but only in speech and her interest in fashion.
- Verbal Tic: Several characters.
- Goombeverly sometimes ends her sentences in a questioned yeah, yeah?
- Ferdinand and Luis like their Gratuitous Portuguese. Olá!
- Fuzzies return with their MEEEEEEEOOOORK!