Young Justice has an exceptional grasp of its own continuity that stretches from its massive mythological elements down to the most minute inside jokes. With so much ambitious self-reference incorporated into the show, it can be hard to trace where many of its subtlest inside jokes began. Case in point: Superboy's hatred for monkeys.
Throughout much of Young Justice, Superboy frequently says "I hate monkeys." To understand why, diehard Young Justice fans may need to turn to the comics set during the show's first season to find the origin of Superboy's seething simian slander.
The joke first appears as early as the fifth episode of the series, "Schooled," where Superboy first utters the line. Tasked with defending a valuable piece of technology that the villain Professor Ivo is after, Superboy expresses his hatred while faced with robotic monkeys invented by the scientist. Ivo calls the devices Mobile Optimal Neural Quotient Infiltrators, or "M.O.N.Q.I.s," and their design is befitting his whimsical sense of flair. They certainly do prove annoying, swarming the members of the Team all at once and proving difficult to stamp down, and from there Superboy goes on to say "I hate monkeys" in several more episodes throughout the show.
He says the line when faced against villainous apes like Monsier Mallah or the Ultra-Humanite in "Alpha Male" and "Revelation," and says it even against the playful green monkey that Kid Flash befriends in "Image." Superboy only briefly reconsiders his stance in "Earthlings" when Beast Boy transforms into a gorilla and aids Superboy's efforts in destroying Krolotean starships. The joke even becomes a frequent occurrence in Young Justice: Legacy, but somewhere along the way fans binging and re-binging Young Justice might be puzzled to learn that the show itself never contained the origin to the line. To find that answer, fans need to turn to issue #2 of Young Justice, titled "Monkey Business."
In the comic, set even before "Schooled," Superboy witnesses an apparent attack on their headquarters of the Cave where the Joker leaves a deadly present for the Team and the Justice League alike. Finding a large wrapped present, the Flash opens the item to discover several green Joker-ized monkeys -- quite similar to the M.O.N.Q.I.s -- which quickly attack the League. What proves traumatic about the battle is that Joker actually gains the upper hand against Superboy's mentors, and the monkeys even manage to harm Superboy himself. To deepen the trauma further, it turns out that the event was all in Superboy's head.
It turns out that the battle did not occur at all, but was merely a psychic simulacrum created by a G-Gnome run amok in the Cave. The genomorph creatures were genetically engineered by Cadmus, much as Superboy himself was, and were used to telepathically program the young Superman clone during his time incubating. Superboy associates the psychic contact with his dark upbringing and proves sensitive to it through the rest of his life, only ever engaging in telepathic contact begrudgingly with Miss Martian at the start of their relationship. The fact that genomorphs themselves look so much like monkeys only further underlines his antipathy toward the creatures. In short, Superboy hates monkeys because they remind him of a moment of vulnerability and all of his worst fears buried in his past.
The comic ends with Miss Martian asking Superboy if he learned anything about himself throughout the adventure, and "I hate monkeys" is his response. The moment is cute and clever, but also shows the deeper and darker side to even the most lighthearted moments in Young Justice.
Such intricate, interconnected lore is the series' forte. Fans delving into such questions are sure to be rewarded when digging back to find such answers. No stone goes unturned and for everything there is an explanation, showing that even monkey business can be serious work.