CLANNAD's story is split into two arcs: the School Life arc and the After Story arc. The School Life arc is where most of the game takes place, and is thus where the majority of light orbs are collected; After Story is only unlocked once all light orbs in the School Life arc are obtained. Ordinarily, light orbs are obtained by viewing a good ending. This guide will list the choices necessary to obtain a good ending for each route, thus obtaining a light orb. However, not all characters' light orbs can be collected in School Life. Some characters, like Fuko Ibuki and Akio Furukawa, have their arcs completed in After Story, requiring multiple playthroughs of After Story to unlock the true ending (for which all light orbs must be obtained). Using the game's skip function (ideally sped up in the settings) will allow you to skip previously read text, saving time.
Between chapters of the game (for which each day constitutes a chapter), you will also see glimpses of the Illusionary World. This story is told from the perspective of a doll made out of garbage (ガラクタの人形 garakuta no ningyou?), who observes the actions of a mysterious girl (幻想の世界の女の子 gensou no sekai no on'nanoko?) trying to survive in what appears to be a wasteland. The meaning behind this seemingly unconnected arc is further explored as the game progresses, through subtle hints in various routes before its culmination in After Story.
Some School Life routes are shorter than others; the game's five main heroines (Nagisa Furukawa, Fuko Ibuki, Kotomi Ichinose, Kyou Fujibayashi, and Tomoyo Sakagami) have the longest routes, and Nagisa's story leads into the game's true ending. Nevertheless, the order of the routes listed in this guide, mixing the routes of main heroines and side characters, is recommended. The game also has bonus routes and other extras (listed in appendices) that don't count toward the game's completion, but are required by achievements and trophies.