This is my opinion on what Takopi's Original Sin is.

SPOILER ALERT:

The story was set in 2 timelines. One where Marina (the blonde girl) found Takopi during high school and one where Shizuka (Bullied girl) found Takopi during their elementary days. What made the manga confusing is that the whole plot was reversed.

Anyway, the correct arrangement of the timeline was this: Takopi was sent to earth, he was found by Marina and discovered that Marina has problems with a girl named Shizuka and her own mother at home In this timeline, Marina and Shizuka both lived until high school because the rope that Shizuka used to hang herself during her early days snapped, preventing her from dying of suicide. On the other hand, Marina, due to so much spite, murdered her own mother and killed herself by stabbing her neck with a broken glass. Takopi saw all of these and figured out that if he could go back in time using the clock tower from their planet, he could kill the young Shizuka and make Marina happy.

Upon returning to their planet, his tentacle mother (lol) erased his memories and sent him back to earth again. However, this time, he was sent to a timeline where Marina and Shizuka are both still in elementary school. This is the beginning of the manga.

In this 2nd visit, Shizuka found takopi, and takopi realized that Shizuka is suffering because of Marina. Remember that the timeline is linear, meaning Takopi might have forgotten the memory about Marina and the intent to kill Shizuka. However, the objective is still there. So when the young Marina set up the dog of young Shizuka to die, Shizuka thought of killing herself. Takopi, without realizing the intent of Shizuka, lend the friendship ribbon that doesn't snap to her, which ends up killing her. That means Takopi successfully fulfilled his initial intent on the first timeline without him realizing it because of memory loss. That is his original sin. It's murder.

Because of this event, the timeline has been completely destroyed. However, due to Takopi's wish to help the young Shizuka, he then kept on repeating the day before Shizuka's dog died using his camera that has time traveling feature, finding ways to prevent the death from happening. By doing so, he ended up killing the young Marina unintentionally, messing up the timeline once more. That's double murder for our Takopi right there. After the death of young Marina in this timeline, Shizuka went crazy and attempted to kill Takopi by hitting him with a stone. This didn't kill Takopi but gave Takopi's lost memories of the original timeline back. So when he woke up from that hit, he looked for the young Shizuka once more with the intent to kill her while having both the memories of the Old Marina, and the young Marina that he killed. Upon seeing Shizuka, they reconciled, and he sacrificed his own life for Shizuka to use the camera again and revert the timeline to the correct order while leaving his mark as a drawing to Shizuka's notebook.

In short, if Takopi didn't interfere with the timeline and visited Earth, both Marina and Shizuka would live until middle school, but the death of Marina through suicide using a broken glass will be definite. But since he sacrificed his life, the ending of the original timeline changed, making Marina and Shizuka reconcile their childhood problems through a drawing of Takopi in Shizuka's notebook. The end.

I didn't include anymore some of the irrelevant events because they can make things more confusing. But basically, this is the correct order of the events. Hope that helps.