故事还有马里奥等人为拯救世界而冒险的其他内容，虽然夹杂着噱头，但比起《纸片马里奥RPG》更黑暗更沉重的故事还有很多，此外还有“宅男”和“自然与文明人” 《马里奥》系列开发了一个截然不同的故事，例如以“共存”和“死后的世界”等主题的剧集出现，以及以“爱”为主题的整个故事。根据主题，关键物品“纯心”不是星星而是心形。
由于舞台是与马里奥世界不同的维度，所以世界观也有很多地方与其他系列有很大不同。例如，故事中出现的古代人更像是炼金术士而不是巫师，而费尔林则是古代人人工创造的有生命的工具，或者是保护纯洁心灵的机器人。古代的过度技术，例如使用（尊巴巴），作为故事的背景而存在。
Disc 1
1 Today's Story
2 The Wedding Begins
3 Wedding Waltz
4 Birth of the Chaos Heart
5 Champion of Destruction
6 Super Paper Mario
7 Mario Bros. House
8 Evil King Bowser Here
9 The Evil Count Bleck
10 Flipside
11 Got a Pure Heart
12 Activating the Heart Pillar
13 And Then... And Then
14 Chapter Introduction
15 Lineland Introduction
16 Lineland Road
17 Underground Room
18 Got an Item
19 Got the Flip Ability
20 Level Up
21 An Unrivaled Battle [8-Bit Mega Star Power]
22 Stage Clear
23 Mount Lineland
24 Perfect Solution
25 Strange Company
26 A New Pixl Joins You
27 O'Chunks, Warrior
28 Ready, Go [O'Chunks Battle]
29 Yold Ruins
30 Got a Special Item
31 Fracktail Appears
32 One Shot
33 Fracktail Battle
34 Soft Light
35 Got a Pure Heart ~ Chapter Completed
36 Count Bleck's Plan
37 In the Darkness
38 Memory 1
39 Get Cooking!
40 A New Partner Joins You
41 Gloam Valley Introduction
42 Gloam Valley
43 Got a Card
44 Outside Merlee's Mansion
45 Merlee's Mansion
46 Look Out for Me
47 Mimi the Copycat
48 Fight Fight!
49 And the Question Is...? [That's My Merlee!]
50 Mimi Battle
51 Happy Flower
52 Goodnight!
Disc 2
1 Bitland Introduction
2 The Open Plane [The Bitlands]
3 Nostalgic Underground [Bitland Underground]
4 Bowser Battle
5 The Tile Pool
6 Big Blooper Appears
7 A Powerful Enemy Emerges [Boss Battle]
8 Dimentio, Charming Magician
9 It's Showtime [Dementio Battle]
10 Butterfly * Collecting
11 Fort Francis
12 Swoon.exe
13 Francis Battle
14 Memory 2
15 Outer Space Introduction
16 Outer Space
17 Whoa Zone
18 Mr. L, Green Thunder
19 Brobot Battle
20 Flopside
21 Land of the Cragnons Introduction
22 Gap of Crag
23 Floro Sapien Caverns
24 Flint Cragley, Cragtrotter
25 Truck GO
26 King Croacus IV Appears
27 King Croacus IV Battle
28 Sammer's Kingdom Introduction
29 Sammer's Kingdom
30 Battle Time!
31 I'm Not Nice [Mimi Battle 2]
32 The Void Destroys Sammer's Kingdom
33 World of Nothing
34 Brobot L-Type Battle
35 Memory 3
36 Tokens, Please! [Flipside Arcade]
37 Forget Me Not
38 Mansion Patrol 1
39 Mansion Patrol 2
40 Mansion Patrol 3
41 Tilt Island
42 Hammer Whacker
43 Mini-Game Over
44 Mini-Game Results
Disc 3
1 The Underwhere Introduction
2 The Underwhere
3 River Twygz Bed
4 The Road for the Lost
5 And the Question Is...? [Dorguy Trivia]
6 Underchomp Battle
7 Underchomp Defeated
8 The Overthere
9 Peach Awakens
10 Overthere Shrine
11 Bonechill Appears
12 Bonechill Battle
13 Memory 4
14 Castle Bleck Introduction
15 Castle Bleck
16 The Evil Count Bleck 2
17 Closing Battle [Count Bleck Battle]
18 Four Heroes Reunited
19 The Destruction of Worlds
20 Promise
21 The Ultimate Show [Final Battle]
22 End of the World
23 Bounding Through Time
24 Proof of Existence
25 Staff Roll
26 Lose Life
27 Game Over
28 Pit of 100 Trials
29 Got a Pure Heart ~ Chapter Completed (w/o Intro)
30 Perfect Solution (Early)
31 Mini-Game Over (Prototype)
32 Mini-Game Over (Early)
33 Underchomp Battle (Early)
34 Unused 1
35 Unused 2
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