In this season all of the mutants are more powerful since their specific powers are increasing with age. The tone of the show is darker and there are less glitzy computer graphics. Their mountain hideout is now a "real" island location rather than a lame computer generated effect. Also, more use is made of stock locations footage, such as New York City and Egypt.
Ashlock, the powerful mutant who was released after twenty-five years in a forced coma, took over Genomax at the end of the first season. In the first episode he taunts hot babe Shalimar Fox (Victoria Pratt) by putting himself in her mind. This really ticks her off. Later, we find out that Ashlock is dying from energy overload and hopes that a witch from three thousand years ago can help him. He manages to clone her and there's a big battle that ends in a bigger explosion. In a time travel episode, Ashlock goes back in time to 1978 so he can change his past and perhaps cure himself. We see that he was a psychopathic kid and that Adam Kane procedure (John Shea of LOIS & CLARK) him caused him to become an even more unstable mutant. That's why he was placed in a coma to begin with. There's a confrontation, the older Adam is killed and for some reason this starts slowly undoing things in the present, like entire sections of the hideout vanishing. So the mutants have to go back in time again, to prevent their leader's death. In one of the more interesting episodes the group encounters a Feral, like Shalimar, who has mutated even more and resembles a werewolf. This, of course, concerns Shalimar, who doesn't want to turn into an animal. Surprisingly, Ashlock is killed when his energy grows too much and he explodes, though he leaves a pregnant girlfriend behind.
The last episode of the season has the reappearance of Mason Eckhart, the villain from the first season. Only he looks completely different, with normal hair and skin tone. He's taken over the company that Shalimar's father owns and is trying to make the perfect human with mutant powers. There's a confrontation and the building they are in explodes (yes, there are tons of explosions this season!), with them all hanging on until there's another blast, which ends up killing half of them. We don't find out who the survivors are until the third season...