The series does have its share of depressing and tragic moments.
- Takuya Yamashiro's father dying in the first episode.
- In the second episode, the alien Garia, who gave Takuya his spider powers so he could fight the Iron Cross Army and turned into a spider to continue talking to him in secret, ends up passing away, which especially stings because Garia is the sole survivor of Professor Monster's destruction of the planet Spider. Takuya responds by vowing to fight the Iron Cross Army to avenge both his father and Garia.
- The tragedy of Kabuton, the Machine Bem Monster of the Week in the ninth episode. Smitten by Takuya's sister and refusing to kill her even under threat from Amazoness and Professor Monster, Kabuton ends up switching the powerful diamond he uses to fuel his laser with her fake pendant to give it to her as a good luck charm—which ends up saving her life by absorbing Amazoness' laser. Tragically, none of them ever realize this and Kabuton is unceremoniously cut down by Spider-Man minutes later.
- The tenth episode has the young woman transformed into a snake woman by Professor Monster begging Spider-Man to kill her, insisting that there's no hope for her. Spider-Man has no choice but to comply.
- The ending of the 11th episode, where the boy that Takuya saved the life of by donating blood has to be relocated so that the Iron Cross Army won't be able to target him anymore, meaning that the two intergenerational friends can't ever see each other again.
- The biker gang leader's father outliving his son and later dying himself, a tragedy which wrings way too close to home for Takuya because of his own father dying and never getting to resolve his differences with his dad before he was killed by the Iron Cross Army.