Routes

The Kagerou Project contains alternative story lines, endings (and in some cases, beginnings) differing slightly through each media. According to Jin, the story has an established backstory, which segues into the Music , then to the Manga , followed by the Novel  , then Mekakucity Actors. Kagerou Daze -in a day's- is set at an unclear point, though likely after Manga Route 2 due to Shintaro having his eye ability.

Backstory
Portions of the Kagerou Project backstory are meant to be mostly consistent (the second manga route partially differs) through the routes. Several songs are included:

xx.xx. (Unknown Month/Day) - xxx (Unknown) Years Before Present

 * Azami coming to existence and creates the Snakes, including the Snake of Clearing Eyes.
 * Azami meets and falls in love with Tsukihiko and gives birth to Shion.
 * Creates the Kagerou Daze and enters.
 * Shinigami Record
 * Shion gives birth to Marry.

08.15. - 1xx Years Before Present

 * Gunjou Rain
 * Marry and Shion are killed and are draw in the Kagerou Daze, and Marry is given Combining Eyes.

xx.xx. - 5 to 15 Years Before Present

 * Kido, Seto, Kano, and Momo all enter the Kagerou Daze and receive snakes.
 * Kido, Seto, and Kano are all taken in as foster children by the Tateyama family, and Ayano forms the Mekakushi Dan.
 * Seto and Marry meet.
 * Shounen Brave
 * Kuusou Forest

Music Route (Songs)
Route XX (bad end) is the canon route and ends with a rewind becoming the manga route. Children Record and Summertime Record serve as the opening and ending of the series.

08.15. - x Years Before Present

 * Snake of Clearing Eyes plans to gather all the snakes in the real world.
 * Ayaka and Kenjirou die, and the later is given the Snake of Clearing Eyes.
 * Dead and Seek
 * Ayano realizes the Snake of Clearing Eyes' plan.
 * Yuukei Yesterday

08.15. - 2 Years Before Present

 * Snake of Clearing Eyes kills Takane and Haruka, and brings the Snakes of Opening and Awakening Eyes to the real world.
 * Headphone Actor
 * Ayano commits suicide and enters the Kagerou Daze, gaining the Snake of Favoring Eyes.
 * Toumei Answer
 * Shintaro Becomes a shut-in.
 * Kido, Kano, and Seto leave their household and make a hideout; Marry joins the Mekakushi Dan.
 * Ene appears in Shintaro's computer.
 * Jinzou Enemy
 * Ene no Dennou Kikou

08.14.00 (Present Day)

 * Momo joins the Mekakushi Dan
 * Kisaragi Attention
 * Mekakushi Chord

08.15.00

 * Snake of Clearing Eyes moves to Konoha's body, killing Kenjirou.
 * Shintaro deletes Ene and commits suicide.
 * Snake of Clearing Eyes kills Hibiya and Hiyori, brings Snake of Focusing Eyes into real world.
 * Kagerou Daze
 * Konoha no Sekai Jijou
 * Clearing Eyes attacks and kills rest of the Mekakushi Dan.
 * Outer Science
 * Clearing Eyes fails to call Favoring Eyes (Ayano), awakens Marry's Combing Eyes.
 * Marry gathers snakes and reloads time.
 * Marry no Kakuu Sekai

Unclear Routes / Placements

 * Lost Time Memory - parts are in Route XX, but parts are in different Routes.

Route 1
Ends quicker than other routes after the Mekakushi Dan go to the amusement park, forcing Marry to rewind time again.

08.15. - x Years Before Present

 * Takane and Haruka present "Headphone Actor" game at culture festival and Shintaro beats her at it.
 * Same events as Music Route.

08.15. - 2 Years Before Present

 * Same events as Music Route.

08.14.00

 * Shintaro goes to mall and gets caught in a terrorist plot.
 * Momo joins Mekakushi Dan and they get involved in the terrorist plot.

08.15.00

 * Snake of Clearing Eyes moves to Konoha's body, killing Kenjirou.
 * Shintaro and Ene join the Mekakushi Dan and go to the amusement park.
 * Clearing Eyes appears after amusement park and kills the Mekakushi Dan.
 * Clearing Eyes fails to call Favoring Eyes, awakens Marry's Combing Eyes.
 * Marry gathers snakes and reloads time.

Route 2
This route is significantly different than most routes. It's the route that shows how Shintaro gained Retaining Eyes and ends with a rewind becoming the Novel route. It's possible this route is actually set before the Music Route because the finale resembles the final scene of Lost Time Memory and Shintaro is shown with his Eye Ability.

xx.xx. - 5 to 15 Years Before Present

 * Marry finds about powers from Azami's journal.
 * Kido, Seto, and Kano meet at the orphanage and are taken in by the Tateyama family.
 * Marry taken into Tateyama household by Seto and joins the Mekakushi Dan.

08.15. - <5 Years Before Present
xx.xx - <5 Years Before Present
 * Ayaka, Kenjirou, and Ayano die in landslide, giving Ayano favoring eyes.
 * Ayano says Marry should be killed, causing Kido, Seto, Kano, and Marry to leave.
 * Haruka and Takane meet and become friends at a hospital.
 * Takane is discharged.
 * Haruka and Shintaro meet and become friends at a hospital.

08.15. - 2 Years Before Present

 * Haruka dies to his illness and enters the Kagerou Daze, gaining his Awakening Eyes and spawns Konoha.
 * Takane attempts suicide by jumping out the hospital window, leaving her body in a comatose state. She then enters the Kagerou Daze and gains Opening Eyes.
 * Shintaro becomes a shut-in.
 * Ene shows up on Shintaro's computer.

08.14.00

 * Shintaro goes to the mall to buy rabbit food for Tono with Ene and Momo.
 * They run into Hibiya and Hiyori on the way.

08.15.00

 * Hibiya and Hiyori are in an accident and enter Kagerou Daze, Hibiya gains Clearing Eyes and Hiyori Focusing Eyes.
 * Shintaro searches for Hibiya and Hiyori and meets Kido.
 * Konoha stops terrorist plot and meet Kano. They find Hibiya passed out.
 * Momo meets Konoha and Kano.
 * Mekakushi Dan investigate the "Kagerou Daze" phenomenon.

08.16.00

 * Mekakushi Dan search for Hiyori.
 * Kano discovers Hiyori standing over Kido's corpse and runs away. Kido was actually killed by Hibiya.
 * Hibiya meets Ayano.
 * Shintaro meets Ayano for the first time.
 * Momo is killed by Clearing Eyes (Hibiya).
 * Clearing Eyes kills Hibiya and takes over Konoha's body.

08.19.00
Notable differences:
 * Shintaro is brought to Ene's incapacitated body and she dies, joining with Haruka in the Kagerou Daze.
 * The Mekakushi Dan initiate their plan to stop Clearing Eyes, resulting in the death of Kano.
 * Marry opens the Kagerou Daze to talk to Azami, but Clearing Eyes kills Seto in the interim.
 * Marry seals Clearing Eyes in the Kagerou Daze.
 * Marry uses Ayano's life to give Shintaro the Retaining Eyes.
 * Marry rewinds time and the story ends with Shintaro waking up on August 15 after many rewinds.
 * Marry joins the Mekakushi Dan while both of Ayano's parents are still alive.
 * Kenjirou Tateyama dies during the landslide.
 * Ayano does not commit suicide and plays an active part.
 * Ayano encounters Shintaro for the first time while he speaks with Hibiya.
 * After her parents death, the Mekakushi Dan leaves Ayano.
 * Haruka, Takane, Ayano, and Shintaro don't go to school together.
 * Haruka and Takane die outside of Clearing Eyes' influence.
 * Route where Shintaro gains Retaining Eyes.

Unclear Route / Placement
At some point, Marry turns Clearing Eyes to stone as Konoha after killing Seto, then rewinds time.

Novel Route (Kagerou Daze)
The novel route ends with Marry being possessed by Azami and attempts to defeat the Snake of Clearing Eyes, but is only able to trap him, forcing a rewind due to the majority of the Dan being in the Kagerou Daze.

08.17.00

 * The Mekakushi Dan, besides Seto, Marry, and Hibiya, are killed by Clearing Eyes or willingly directly enter the Kagerou Daze opened by Azami.
 * Azami takes over Marry's body, trapping Clearing Eyes, but not defeating him.
 * Mekakushi Dan communicate over the phone and decide to reload time, implying they'll defeat him next time.

Mekakucity Actors Route
The placement of the anime route is set after the Music, Manga, and Novel routes and incorporates them by showing them off as other rewinds. This route originally reveals that Shintaro was given Retaining Eyes in Manga Route 2 by Marry. It ends with the defeat of the Snake of Clearing Eyes.

08.15.00

 * Shintaro brings Ayano out of the Kagerou Daze.
 * The Mekakushi Dan manage to finally overcome the Clearing Eyes and force him to grant Konoha's wish to save Hiyori, and becomes a surrogate for her.
 * Kenjirou reunites with Ayaka, which completed his wish.
 * All Mekakushi Dan members are alive besides Konoha, and Haruka's silhouette is shown among them.

Kagerou Daze -in a day's- Route
It's unclear when this route takes place, though likely after Manga Route 2 due to Shintaro having his eye ability. Sidu said this route has a sequel called "route-2", but did not go into detail. Besides character design changes, this is an alternate version of the terrorist plot. There is notably a member of the terrorist group that has an eye ability, which Shintaro noticed. He and the Dan mistook the leader as having the eye ability, but after the incident he realized it was someone else. A bomb goes off in the building at the end of the movie, leaving what happens unclear.

Good End and Beyond
Eventually, Clearing Eyes is defeated, with the Mekakushi Dan (besides Konoha) and Haruka surviving. This outcome is currently only shown in the MCA Route and in the ending theme Summertime Record. It is shown in MCA and in the post-Summertime Record chapter Lost Day Hour that Ayano and Hiyori survive as well. Jin has expressed interest in writing about a "new Mekakushi Dan" in the future.

Post-Summertime Record Material
 * Lost Day Hour (chapter)
 * Lost Day Hour
 * Remind Blue