There two routes, one is is Route 1 and the other is Route XX. Route 1's Shintarou wears a red jacket, while Route XX's Shintarou wears a black hoodie jacket.
In Route 1, Shintarou spoilt his computer by spilling his drink (thanks to Ene) and went out to buy a new one. After, he meets the Mekakushi Dan. In this route, he slowly gets out of his hikikomori habits and becomes a member of the Mekakushi Dan. Here he also gets over his best friend (Ayano's) death, as he form new bonds with the Mekakushi Dan. An incident shown in the song is when Kuroha takes over Konoha's body, and tried shooting himself in the head, in hopes of killing Konoha. But it is interrupted by Shintarou, who takes the shot instead, either killing him or having him half dead,much to Kuroha's surprise (well maybe).
In Route XX, Shintarou does not accept Ene and is successful in deleting and blocking her out of his devices. Since Ene is not there to have him spill his drink, Shintarou's computer does not spoil and he continues his hikikomori days while still grieving and regretting over Ayano's death, since he thought that he could stop her from committing suicide when he saw her crying before the event happened. He kept seeing Ayano in his dreams, showing that he still could not accept her death. He keeps telling himself, "I don't care, go die, go die". One day, he then took notice of a pair of scissors on his table. Then, he attempts to kill himself by slitting his own throat. Then, he falls back on his bed, either successful in trying to kill himself, or falling in resignation. But the highest possible is that he was successful, or else he would not have been able to enter the 'Heat Haze'.
This is the most crucial part of the story. Apparently both Shintarous had died at the same time, matching the qualifications in entering the 'Heat Haze' to get his eye abilities. As both Shintarous wake up, they see Azami, asking them of their current 'wish'. As Route XX's Shintarou sits up and thinks, Route 1's Shintarou had just walked past her, much to her surprise and due to his actions, both Shintarous are transported to their old classroom. Instead of having Ayano's table having a vase of flowers on it, the rest of the tables except Shintarou's and Ayano's tables, have vases of flowers on them. Both Shintarou's then face Ayano, who was at her seat. Route 1's Shintarou walks up to her and talks with her. She (maybe Azami) asks "Can you hear me?" Then she tells him, "I died. I'm sorry." "Shall I say 'goodbye'?"and Shintarou says "Goodbye." with a smile on his face, clearing his regrets and guilt as he had confirmed that it was not his fault that she had died. Ayano is surprised by his smile, but she smiles back at him and places her trademark scarf on him, along with passing on her eye ability to him. Route 1's Shintarou opens his eyes, and his eyes are red, showing that he currently has an eye ability. On to Route XX's Shintarou. He sees Ayano, and she tells him "I died. I'm sorry." "Shall I say 'goodbye'?" Shintarou, is shocked,since after so long he got to see her and here she was, telling him goodbye. Unable to get over her death, he tells her "Don't say such lonely things" and "Don't go away". He is unable to reach her, and gets transported back to his room, and the time and date on his clock is the same as before, showing that his current world is stuck in the time-loop. In the video it is also shown that in Route 1, in Mekakushi Dan, Ayano is seen for a short moment and dissapears. It is proven by other theories and by own observation that it was impossible for Shintarou to see her, since she was dead. It was Kano using his eye ability (Deceiving Eyes) to allow Shintarou to see Ayano to mentally torture him, since Kano thought that Shintarou was the reason why Ayano committed suicide. Either that, or Shintarou is just imagining things.
Route XX, roman numerical, means Route 20. That being said, it is possible there were many more routes and in some way or another, the Shintarous of all the routes are 'connected'. Considering his personality and Route XX's Shintarou, it is possible he killed himself in other routes as well. Shintarou had wished that he stayed in the days where Ayano had not died yet, a possible cause of the time loops. In Route 1, when Shintarou saved Konoha, it is likely he 'remembered' about the time loop, and would wake up alive again the next day but ends up facing Azami, and probably surprised her since he died so many times and expected him to wake up again in the loop, making his case 'special'. Ayano died most probably at the same time Haruka and Takane did, activating the 'Heat Haze' sequence. In exchange for Ayano's life, the other two got eye abilities. But still, Ayano got the eye abilities. She probably committed suicide in hopes of getting an eye ability after looking through her father's reports. Another theory of the song is that Route XX's Shintarou is Shintarou's past self, and Route 1's Shintarou is Shintarou's current self, and the two are somehow 'co-existing' with one another. This theory is not mine, so I cannot really elaborate it, unfortunately.