At her father's training and urging, young Kara has done appalling things. She murdered children, took the life of her own mother and now she cannot assimilate herself into Earth's societies, as a girl or as a Superhero. She's lost, hurt and confused. In the darkness, her father begins to tell her why.
She had a happy childhood with her mother and father, both of which loved her very much. She idolised her scientist father but he was ever the rival of his brother, Jor-El.
Zor-El hated the thought of what his brother had done in discovering the Phantom Zone. He was horrified at the idea of sending criminals into a place that was no better than a living death. He would rather those criminals be put to death. But the Council praised Jor-El and began using the Zone as the main form of punishment for all types of criminals.
As the Zone was utilised more frequently so Kryptonian society began to fall into degradation. Argo City, the site of the first banishment, was the worst hit by these horrors.
One night, Zor-El is leading his wife and daughter home through an area that had once been clean and safe. They're attacked by a group of muggers but when Zor-El uses the sunstone crystal that he keeps around his neck to slay them, they die. He's suddenly hit by the realisation that these men were, in fact, possessed by some kind of phantoms, infecting Krypton from the Zone.
He became obsessed with finding these creatures, working out how to kill them. He goes to his brother, begging for help against the ghosts. Jor-El has discovered that the planet is dying, being ripped apart by ground-quakes, but he denies Zor-El, saying that his rantings are madness.
As Zor-El worked on in secret, he pulled his daughter along with him. Her unwavering faith in her father was what drove him. He began to run tests on her, fusing her with the sunstone crystals. She was bullied, an outcast by her peers.
Zor-El discovered that the phantoms had started to infect children and he sent Kara out to kill them all. She slaughtered all of her friends. The family are arrested.
At the sentencing, Krypton finally begins to tear itself apart and they go free. The phantoms have revealed that the only way they will rest is if the entirety of the House of El is destroyed. Zor-El sees the light at the end of the tunnel. Just when he begins to believe that the phantoms will be gone forever, Jor-El reveals his plan to send Kal-El, his son, away in a ship. The House of El will live on.
No matter how he begs, Zor-El cannot convince his brother to change his mind. And so, just as Kara is forced to slay her mother because she has become infected by the phantoms, he sends her away. Her mission is to kill the last of the House of El and finally cleanse the universe of these phantoms.