The skull guy who was created by Arnos 2000 years ago wanted to use the fusion magic he was working on to artificially produce a strong enough vessel for the fake Demon Lord to reincarnate in. The idea in this case is to separate one soul into two, have each individual piece get stronger over a period of time, and then have them merge into one once that period of time was over. The only problem with it is the fact that his fusion magic has a time limit, a very short one at that, so it'd be impossible to get the split souls to stick together properly. In addition, the laws that magic follows in this series also limits how long you can even keep the soul split to begin with, so before he could deal with the issue of sticking them back together after too long a period of time, he'd have to deal with the issue of keeping the soul split long enough to even deal with that issue, else they'd automatically reconnect in moments, which is too short to actually do any strengthening.
This is where he gets the genius idea of splitting the soul of a fetus. The logic following that, by splitting the soul before it's even recognized by the world, the world will instead recognize it as twins. Following that loophole, by applying the fusion magic to happen years later, the split soul would actually fuse back together permanently as a result of the world fixing the error caused by the loophole. This is what results in the birth of Sasha and Misha.
However, despite being raised with this knowledge since birth, Sasha has never once actually hated Misha and, after going through as much as she did growing up, started to get the idea that it would be better for her to disappear instead. So she started to plan for a way to alter the spell so that instead of Misha being merged into Sasha, she'd be merged into Misha. The plan finally came into fruition when Misha got her the Phoenix robe, as it would strengthen her enough to the point that she could reasonably pull it off. And to make sure that when she'd merge into Misha, that Misha would feel no regrets about her disappearing, Sasha went the route of attempting to kill Misha as a way to forcefully make sure that Misha would hate her.
Of course, Arnos, points out a way to override the spell so that it would be impossible for Misha and Sasha to fuse. However, that requires using Time magic, and the entity that presides over it tends to get really pissed off at anyone who messes with time. In addition, the founder that Arnos created is still brainwashed, and doesn't want Arnos to succeed in stopping his spell, so he had already snuck in the secret passage ahead of time and was hiding out so that he could forcefully stop Arnos. The Time god takes advantage of this and fuses himself with the founder to take on Arnos. After a fight, Arnos defeats the two, and gets rid of two of the souls in the founder's body: the time god's and the guy who brainwashed him. This leaves the original soul of the founder free, who them swears his loyalty to Arnos again before becoming a spy of sorts, since all the higher ups on the outside believe he died fighting Arnos.
Meanwhile, Arnos successfully sends Sasha and Misha back in time to have them fuse with their souls just after they were split in the womb, resulting in them becoming actual twins instead of just a split soul. It also doubles as them accepting Arnos as the Demon Lord as in order for the spell to be successful, they had to believe in the fact that Arnos was the actual Demon Lord for their origin magic to work.