Both Sekai's father and mother are son and daughter of Tomaru, and so is Setsuna.
To make it even worse, Sekai's mother was born between Tomaru and another of his daughter.
So her mother is a product of incest between Tomaru and one of his daughter, and she herself had incest with her own half-brother, one of sons of Tomaru, and thus Sekai was born.
It's a very, very complicated and twisted world.
But surprisingly, in a world where half the characters seems to be products of cross-generation incests, Makoto isn't one of them.
Btw, Sekai and Setsuna's father are the same guy, Shun Hazama, son of Tomaru, making them half-sisters.
Shun and their mothers are in the game Summer Radish Vacation.