Milo Murphy's Law contains several story arcs across its first and second seasons, that connect several episodes in the show's run to each other with a progressing, underlying story. Some of these story arcs span over a small group of episodes, while others are the focal point of a season. It is not uncommon for story arcs to overlap one another.
- NOTE: Keep in mind that the story arcs have conjectural names as a way to distinguish the arcs from each other; official names have yet to be given.
These story arcs form the show's overarching and evolving story.
|B.O.T.T. Introduction Arc||A mini arc about the introduction of Vinnie Dakota and Balthazar Cavendish. It starts with "The Doctor Zone Files" and ends with "Time Out".|
|Counteragent Arc||A primary mini arc following the B.O.T.T. Introduction Arc, in which Cavendish is convinced Milo is sabotaging his and Dakota's pistachio missions. Starts with "Time Out" and ends with "Missing Milo".|
|Pistachions Arc||A major story arc that centers around the malevolent, mutated pistachio trees known as the Pistachions. Preludes with "The Substitute", properly begins with "Missing Milo", and ends with "The Phineas and Ferb Effect".|
|Doofenshmirtz Arc||A primary story arc focusing on Heinz Doofenshmirtz from Phineas and Ferb, learning that he'll invent time-travel and preparing for it. It starts with "The Phineas and Ferb Effect" and continues throughout Season 2.|
|P.I.G. Arc||A story arc centering around Cavendish and Dakota being hired by Bob Block to collect alien trash after getting fired from the Bureau of Time Travel. It starts with "Picture Day" and continues throughout Season 2.|
|Octalians Arc||A major story arc in which cephalopod-like aliens from Octalia discover the negative probability ions surrounding Milo, and wanting to use Milo for some kind of goal. It starts with "Managing Murphy's Law" and ends with "Sphere and Loathing in Outer Space".|
|Forsaken Perry Arc||A story arc nested inside the Doofenshmirtz Arc, in which Doofenshmirtz feels betrayed by Perry the Platypus after he finds out the Organization Without a Cool Acronym pays him to watch over Doofenshmirtz, ending their still new friendship. It begins with "Sick Day" and ends with "Milo in Space".|
|Rogue Cavendish Arc||A story arc following the P.I.G. Arc, in which Cavendish, after no one believing him witnessing an alien abduction, is sick of being stuck with inconsequential jobs, and decides to leave P.I.G. and his partner Dakota behind, to spread word about the aliens and become a hero. It starts with "Abducting Murphy's Law" and ends with "Milo in Space".|
These story arcs form side stories that span throughout the show's run. Some tend to be relevant to any of the primary story arcs listed above.
|Llama Incident Arc||A minor story arc which purpose is to hint about a past event known as the Llama Incident. The Llama Incident was first mentioned in "The Undergrounders", and mentioned in several other episode until the eponymous episode details it.|
|Milo and Amanda Arc||A secondary, series-wide arc about the relationship between Milo Murphy and Amanda Lopez. It starts with "Smooth Opera-tor" and continues throughout Season 2.|
|Mr. Drako Arc||A minor arc concerning the question whether Kyle Drako - one of Milo's teachers - is an actual vampire, or just an eccentric human being. It starts with "Athledecamathalon".|
|Just Getting Started Arc||A secondary arc that centers around Zack starting a band with Milo and Melissa. It preludes with "Secrets and Pies", begins with "Battle of the Bands", and continues throughout Season 2.|
|Lost Dakotas Arc||A minor story arc about Dakota and several paradoxes of him, created each time he traveled back in time to save Cavendish. It starts with "The Island of Lost Dakotas" and presumably ends with "Snow Way Out".|
|Primary||B.O.T.T. Introduction Arc • Counteragent Arc • Pistachions Arc • Doofenshmirtz Arc • P.I.G. Arc • Octalians Arc • Forsaken Perry Arc • Rogue Cavendish Arc|
|Secondary||Llama Incident Arc • Milo and Amanda Arc • Mr. Drako Arc • Just Getting Started Arc • Lost Dakotas Arc|
|Secondary Story Arc Episodes|
|Llama Incident Arc||The Undergrounders • Rooting for the Enemy • Murphy's Lard • We're Going to the Zoo • Battle of the Bands • The Llama Incident • Missing Milo|
|Milo and Amanda Arc||Smooth Opera-tor • School Dance • Cake 'Splosion! • Managing Murphy's Law • Spy Little Sister! • Ride Along Little Doggie|
|Mr. Drako Arc||Athledecamathalon • We're Going to the Zoo • School Dance • The Math Book • Some Like it Yacht • Backward to School Night • Milo Murphy's Halloween Scream-A-Torium! • Picture Day|
|Just Getting Started Arc||Secrets and Pies • School Dance • Battle of the Bands • Disaster of My Dreams • Managing Murphy's Law|
|Lost Dakotas Arc||Backward to School Night • Love Toboggan • The Island of Lost Dakotas • The Phineas and Ferb Effect • Snow Way Out|
|Episodes in Italics indicate an episode that doesn't center around the subject of an arc but is still related to it.|