Miss Martian, Superboy and Lagoon Boy was the main love triangle throughout the second season of "Young Justice".

In the beginning of the series, Miss Martian and Superboy became founding members of a covert team for the Justice League, consisting of their protegees. Since they first met, Miss Martian and Superboy soon started to develop romantic feelings for each other and later began a private relationship. They had fallen in love and were the very first couple on the team of young heroes. The relationship between them lasted for 5 years until Superboy broke up with Miss Martian shortly before the beginning of the second season. Following their break up, Miss Martian and Superboy's relationship became very strained although they still managed to maintain professional when working together on the Team. However, not long after their break up, Miss Martian began dating Lagoon Boy, one of the newest members of the Team and ever since established the love triangle.

Miss Martian appeared to be happy with Lagoon Boy as they were open and affectionate in front of everyone and Lagoon Boy began calling Miss Martian a sweetheart nickname, "Angelfish". Superboy was not happy with their relationship and showed obvious signs of anger, jealously and disgust whenever he saw them together. Although he did not like Lagoon Boy and saw him as a jerk, Superboy did acknowledge that he does treat Miss Martian right, but also knew that what they had was nothing more than a rebound romance despite Miss Martian's protests. Lagoon Boy made his dislike of Superboy very clear and well known as he always felt uneasy whenever Miss Martian and Superboy were alone together and always enjoyed rubbing their new romance in front of Superboy, completely aware of his discomfort. However, it clearly shows that despite their break up and her new relationship with Lagoon Boy, Miss Martian and Superboy are still deeply in love with each other, but simply try to ignore their feelings.

For the longest time, the details about the end of their relationship were unclear for sometime until the truth behind their break up was eventually revealed. When Miss Martian had fully mastered her psychic powers, she began to abuse them by attacking her enemies and willingly leaving them in catatonic states. Superboy was appalled and felt Miss Martian was behaving no better than her arch-nemesis, Psimon. However, Miss Martian refused to admit her wrongdoings, believing her actions to be justified and while Superboy was not happy with her, he did not report her to the Team or Justice League, hoping he meant more to her that could convince her to stop. Unfortunately, Miss Martian instead decided to tamper with Superboy's mind to make him forget that he was ever upset with her in a desperate effort to save their relationship. However, due to the strong psychic bond that was created between them in the past, Superboy was not affected and instantly recognized Miss Martian's psychic touch.

Superboy was left deeply hurt and betrayed by Miss Martian's actions, heartbroken she would go so far as to violate their special connection. Realizing her actions towards him was the last straw, Superboy ultimately broke up with Miss Martian, feeling as though she left him with no other choice. Although she has since felt a great guilt over what she had done, Miss Martian still refused to admit her abuse of power and continue the rogue use of her telepathy for most of the second season against the Team's enemies. However, it wasn’t until attacking Aqualad did she finally start to realize the error of her ways. Believing him to be a traitor and the murderer of her best friend, Artemis, Miss Martian left him catatonic, only to be shocked and devastated to learn the truth about his and Artemis's role in the deep cover mission to infiltrate the Light.

In the aftermath of the attack, Miss Martian was traumatized to the point she refused to use her powers and began to pull away from Lagoon Boy. Superboy quickly noticed the change in her and soon Miss Martian began to seek comfort and confided in him about her actions towards Aqualad, finally realizing Superboy was right all about her abuse of power. Lagoon Boy quickly grew jealous, seeing not only had Miss Martian began avoiding him, but realized that she and Superboy were starting to grow close again and attempted to confront her about their relationship. However, they were soon interrupted by the appearance of Deathstroke and Tigress, who kidnapped Miss Martian to restore Aqualad's mind.

Following weeks of captivity, Miss Martian had time to gain clarity over her wrongful actions and by the time of her escape, she had fully come to terms with everything she did and set out to atone for her mistakes. Miss Martian ended her relationship with Lagoon Boy, finally admitting they never had a real relationship together to begin with. Miss Martian confessed the only reason they began dating was because Lagoon Boy made her feel better about herself after all the horrible actions she committed throughout the season. Although he tried to reason to give their romance a chance, Miss Martian refused and fully acknowledged him as nothing more than her rebound boyfriend.

Miss Martian had also realized she was still in love with Superboy and intended to fully reconcile and renew their relationship. By the end of the season, Miss Martian apologized to Superboy for her actions and finally, their relationship was on the road to recovery, bringing an end to the season long love triangle and reuniting Miss Martian and Superboy at long last. A few years later, Miss Martian and Superboy's relationship is fully restored with the couple happily married while Lagoon Boy returned to Atlantis and found real love for himself.