They appeared in the Fifth and Sixth Seasons and were the main antagonists in the Season 5 premiere "Arrival".
The Disciples were Zod's closet allies during the civil war against Black Zero on Krypton. While General Zod was head strong and very calculating on planning attacks, his disciples acted as his counselors conversing with him on the best strategies of attack. When Zod was captured, the disciples contacted the Brain InterActive Construct who informed them that Zor-El planned to destroy Krypton and to flee the planet quickly.
The Brain InterActive Construct told them to follow Jor-El's son, Kal-El, to Earth where they would use him to free Zod and turn the planet into a Kryptonian paradise. Aethyr and Nam-Ek fled Krypton in the Black Ship along with Brainiac but it stayed motionless in the dark part of the cosmos awaiting for a sign.
After Lana Lang, who was possessed by her ancestor Countess Margaret Isobel Thoreaux, killed Genevieve Teague with the Crystal of Air, it was stained with blood and alerted the Black Ship that the Stones of power were on Earth and the ship headed to Earth. The Black Ship had arrived in Smallville during the midst of a second meteor shower.
Lana Lang had witnessed the Black Ship crash land in a field and saw two Kryptonians come out of the spaceship. The Smallville police force arrived and surrounded them but they blast all the police cars around them with heat vision. One officer managed to survive named Greg Flynn. After disposing of the police, the Disciples super-speed into the Kawatche Caves where they encountered Lex Luthor asking him if he was Kal-El.
They determined he was not Kal-El as Lex bleeds, taking the key from his hand and left abruptly. They traversed Smallville in search of Kal-El, leaving a trail of destruction and brutality in their wake. The Disciples then went to the Smallville hospital continuing their search for Kal-El. Lois Lane tried to confront them, but Aethyr chokes her and threw Jonathan across a room.
Lana appears and lures the Kryptonians to the mansion, saying she knows where Kal-El is. She tried to trick them into entering Lex's vault full of kryptonite-rock artifacts, but Nam-Ek managed to stagger away from the vault and regained his strength, long enough to replace the lead-lined door.
The two recover and throw Lana across the room. Clark arrives at the Mansion and the two believed themselves to be the last survivors of Krypton and wished Kal-El to join them in making Earth into a new Kryptonian paradise. After Clark refused, Aethyr throws a wrist ring off her arm to form a vortex portal to the Phantom Zone to trap Clark in it. However, Clark strongly resists and managed to knock them into the portal they opened, in a bit of poetic justice; their brutal methods had come back to haunt them.
Months later, when Kal-El was exiled to the Zone, the two disciples confronted him, seeking revenge for their imprisonment. They blamed him, when it in reality it was their own fault for opening the portal in the first place. The two wished to execute him immediately, but Raya's quick witted deception convinced the two that he could free them from the Zone.
At the last moment she betrayed them, slicing open Nam-Ek's throat, killing him while telling Clark to take the portal back to Earth. Aethyr however came behind Raya and stabbed her in the back as Clark escaped through the wormhole. Nam-Ek died and Aethyr remained trapped in the Phantom Zone.