While Martin is at the Center cleaning out cages in the Creature Containment Facility (a "mission" M.O.M. has bestowed upon him), he is scratched by the Phantom Werewolf.

Martin uses Center technology to catch girls and gets in trouble for it by M.O.M. and has to clean cages as punishment. Martin decides to do the "empty" cage first and starts to clean it but a werewolf is actually in the cage. Martin and the werewolf struggle for a while but then Martin gets loose and gets out of the cage but gets scratched in the process. He begins to have side effects such as a longing for food next itchiness due to sped up hair growth then sensitivity to certain sounds and increased smell distance.

After this several students go missing and then Martin and Diana find out about it. Next Martin starts to figure things out while Diana rushes to Java to see if he has seen Martin. Then Diana and Java investigate Martin's room and find some things that lead them to think that Martin is hiding a creature. Diana and Java then see something dragging a person outside from a window and start to go after it but then find out that martin is a werewolf. Diana and Java try to help Martin but he refuses saying that he doesn't want to be caged up like those creatures at the center and says he will "go somewhere he can't hurt people" and runs off but before he can get to far Diana puts a tracer on him without Martin knowing.

Diana and Java then talk to M.O.M. and tell her that Martin is a werewolf and M.O.M. lets them know that the alpha wolf escaped from the Center. Java and Diana then start to follow Martin and eventually find his footprints leading into a cave they all tell Martin of the werewolf hunting all the alpha males in the area. The werewolf then comes in on them and Martin and the werewolf fight with a little help from Diana and Java. They all end up trapping the werewolf in a cage. Then everything goes back to normal but Martin is still a werewolf and tries to take the cure but instead ends up drinking Diana's hair growth serum instead.

When people begin disappearing from a residential development, M.O.M. calls Martin, Diana, and Billy in to investigate. They trace the disappearances back to a packet of sea monkeys that were contaminated by the town's toxic water supply.

Martin, Diana, Java, and Billy investigate reports of strange little creatures terrorizing a nearby town.

Torrington's old biology teacher, Mr. Black, allows himself to be bitten by a spider, transforming him into a half-spider half-human creature to get revenge on the staff who forced him into "early retirement" because of the unorthodox/non-Torrington approved experiments he was performing in his lab. (The spider was really a spitting spider, which is why it is shown that Mr. Black was able to fire a web thread from his mouth.)

Also, Martin is completely thrilled and maybe they'll finally get some new blood (preferably of the female variety) to teach the class.

When Martin shows Diana some new "supernatural artifacts" he ordered off of the internet (also in the website, Awesomejunk.com), she barely has time to notice. In fact, she's so overwhelmed with life (homework, clubs, social life, job at the Center), that she off-handedly makes a wish that she could be in two places at once. Later, to her complete shock, she finds that her wish has come true: Diana has a new roommate - herself!!!

When Martin and Diana take a class trip to the Math Museum, their bus breaks down. They quickly realize the town they've landed in is only inhabited by teenagers. At first they (and their friends) think it's totally cool... until Java goes missing and Martin gets a strange instant message begging him for help!

A teen named Damien in Mapleton, finds a website, Creeping Revelations that is inhabited by an evil alien named Vargos. Damian, his friends, Martin and the gang, and some other teenagers are all that remain. People who are older than 18 are sacrificed and digitized as energy for the evil alien. Java is captured by Damien and his friends and they suspect Martin and Diana of getting too close to finding out what they are doing so they try to sacrifice them as well but they escape.

After that, Martin and Diana meets the Resistance led by Damien's sister, Haley who helps them fight the now mutated Damian and Vargos. Martin goes to distract Damian while Haley and Diana disable the website. The mutated Damian goes after his sister but Diana tries to save Haley and gets digitized so Haley can finish deleting the website. Vargos himself appears to defeat them but Martin tricks him and is sent back into the computer and everyone that was taken was returned.

When Darla, a lonely student and one of Torrington's least popular and least confident co-eds, gazes into an old mirror that she finds in the school's drama department and makes a wish (to be beautiful and well-liked like Jenni), her "wish" comes true!

The Monsters of The Gateway are about to capture and eat Martin, Diana, and Java. However, Java notices that when Martin powered up his u-watch, it causes a disruption in the energy shield that evil M.O.M had created. They used this to their advantage and were able to slip through the opening, and were able to escape out of The Gateway, with the monsters in close pursuit. Billy, who is observing them back in The Center, was able to open up a portal doorway back to M.O.M's office, and the three of them manage to fall through. The door shuts before any monsters get through.

When M.O.M. ceases to return from her Jamaican vacation, Billy calls in Martin, Diana & Java to investigate (despite the fact that Martin has been temporarily suspended from the Center). They uncover what M.O.M. was really up to – she was on a secret mission to unlock the Gateway to the Underworld!

While sick with a mysterious illness, Martin, Java & Diana are quarantined in the Center's medical wing and reminisce about their past adventures. Due to a misunderstanding they think M.O.M. has decided to terminate them before they can spread the sickness and flee deeper into the Center unaware that the real cause of the alarm is that the Boogeyman has escaped and they're heading right for him!

The gang is quarantined by a mysterious illness at The Center and M.O.M. wanted to terminate the gang before they spread the sickness. As of now, they are trapped in the hospital. However, the real problem is that the Bogeyman has escaped and been the one that cause the false alarm. The Bogeyman is heading in to the Center and the agents have no idea!