After all the villains had escaped during the breakout, Black Phantom stayed in the Hero Factory. He then sent his duplicated Arachnix Drones to trap the mission managers and revealed himself to Zib. He then claimed the factory was his now that all the heroes,except for Rocka, had left to capture the villains. Then he set up the Fail Safe Shield around the factory and locked every room as well to make sure no "unwanted visitors" would enter, and forced Zib to tell Rocka, who was in the villain storage room, that it was all a safety procedure. Black Phantom later realized Rocka had escaped through the elevator shafts and sent his drone to go after him. While the duplicated Arachnix went after Rocka, the villain revealed his plan to the mission managers: to steal the plans for the Hero Factory so he may build a factory for villains and to also destroy the Hero Factory. Zib then stated his plan would not succeed because the Quaza would recognize him as a villain. Black Phantom then revealed to them he had Anti-Quaza and used it shut down the mission managers. He then plugged himself to the assembly tower in an attempt to destroy the factory, only for Rocka and the rest of the Alpha 1 Team to enter. Rocka climbed up to Black Phantom and plugged more wires, the villain then
He, along with Toxic Reapa, XT4, Thornraxx, Splitface, Jawblade, Voltix, Core Hunter, and Speeda Demon, wanted to find the Tree of Harmony and use its magic for their own evil purposes. To do this, Black Phantom planted some strange seeds called Plunderseeds, which took a long time to sprout until the day Twilight was supposed to perform her first debut in the Summer Sun Celebration. The Plunder Vines captured Princess Celestia and Princess Luna and Black Phantom was able to get into Canterlot and find the file containing the location of the Tree of Harmony and used it to find his way there. He then went to Ponyville and found Twilight and her friends using the Elements of Harmony and decided to use them to power the Tree of Harmony and had Voltix and the others guard them while he plugged himself into the Tree of Harmony to transfer all its magic into him. But he was foiled when Stormer, Bulk, Stringer, Furno, Surge, Breez, Nex, Evo, and Rocka and the Mane Six plugged him in more and eventually overcharged him and he was defeated and was cuffed. However, before his defeat, he managed to send the file containing the location of the Tree of Harmony to an Unnamed Villain, who plotted to destroy it using his brains.
He, Toxic Reapa, XT4, Thornraxx, Splitface, Jawblade, Voltix, Core Hunter, and Speeda Demon returned to take over Equestria by altering the past, but Stormer, Bulk, Stringer, Furno, Surge, Breez, Nex, and Evo defeated and cuffed Speeda Demon, Core Hunter, Voltix, Jawblade, Splitface, Thornraxx, XT4, and Toxic Reapa, leaving Black Phantom to alter the past himself and Optimus, Twilight, Starlight, Rocka, and Spike went to stop him. They arrive on the day Rainbow Dash was about to perform her first Rainboom. Black Phantom was able to trick Starlight and Twilight into stopping Rainbow Dash from performing the Rainboom, resulting in many alternate timelines, like Fire Lord, Drilldozer, Nitroblast, and Jetbug successfully taking over the Crystal Empire, Von Nebula successfully defeating the Princesses and taking over Canterlot, and Pythor and the Overlord successfully having all the magic in Equestria for themselves. Later, the five eventually manage to defeat Black Phantom. Refusing to accept defeat, Black Phantom grabbed Twilight by the throat and forces Starlight to make a choice: Join him and rule at his side or her teacher falls to her death. Starlight thinks then says no. Black Phantom tries to reason with her but Starlight reveals that she has seen what Black Phantom has been able to do, even without his comrades at his side. Black Phantom was surprised to hear that she was spying on him and his followers and learn about what they were capable of. Black Phantom looked as if he was giving up, but when kind words from Spike, Rocka, Optimus, and Twilight were thrown at Starlight, he pounced on her and was about to grab the object when Stormer appeared and cuffed him. Black Phantom was