The following is a list of the story arcs found in the main section of El Goonish Shive.
Note that the term "story arc" is based on usage in commentaries for EGS itself, for example EGS Main Story Comic for 2012-03-05 specifically mentions Summer being story arc and The End of Spring as story line.
- El Goonish Shive
- Sister
- New and Old Friends
- Night Out
- The Morning After
- Painted Black
- Shadows After Dark
- Before The Party
- Grace's Birthday Party
- The After Party
- Hidden Genesis
- Sister II
- Q&A 4
- Bringing Silly Back
- Q&A 5
- 9001% Serious
- Summer
- The Dawn
- Pandoras Box
- Sister 3 - Catspaws
- Guest Comics
Canonicity
Most, but not all main story lines are canonical:
- El Goonish Shive includes non-canon April Fools Week and Q&A 1 which is Q&A
- New and Old Friends includes non-canon II slooF lirpA
- The Morning After includes Q&A 2
- Painted Black includes Special Features, which are more like Q&A
- The After Party includes ... actually, consists of Q&A 3, which is Q&A
- Q&A 4 is Q&A
- Q&A 5 is Q&A
- The Dawn includes Q&A 6, which is Q&A
- Pandoras Box includes Q&A 7, which is Q&A
- Guest Comics are, well, guests comics and completely non-canon