Jafar brings Alice's father to Wonderland but realizes with the two estranged that the plan won't work, so he magically becomes him. 

Alice is leery of her father but just as she starts to warm she realizes this is an imposter. Her father always said grace before every meal and didn't this time. 

Jafar brings her real father who apologizes to Alice for not believing in her. He also tells Alice that he overheard that Cyrus escaped his prison. When Jafar throws the man off a cliff, Alice uses her second wish to save him. 

In Jafar's past we see him go to find his father, the sultan after his mother dies. His father makes him a servant but when Jafar let's it slip to others that he is the man's son, the Sultan tries to drown him and has his body thrown out with the trash. But Jafar survives.

In present day Wonderland, Jafar's father is the man in the other cage that was next to Cyrus. Jafar refuses to let him die.