Secrets and Openness
Dr. Hatch, in his attempts to recruit the members of the Electroclan to his twisted ways, employs the use of persuasive arguments, but these arguments pick and choose from the whole truth, making his position seem more relatable and morally justifiable than it, in fact, is. He presents a façade of openness but is actually keeping many secrets from them. The heroes themselves keep secrets from Hatch, such as the fact that Grace downloaded the mainframe of the Elgen computer, as well as the new powers Michael and Taylor develop.
The theme of openness also comes to light with the impact of Taylor's electric powers. She can read minds, so she forces openness, even on those who wish to keep secrets, such as the man the Voice sent to pick up the hard drive. The relationship between Michael and Taylor is an incredibly open one; there can be no secrets when your girlfriend can read your mind.
Family Ties
Michael clearly loves his mother, and he goes to extreme lengths to save her. While in his apartment in Idaho, he pauses to reminisce with a photograph of her; the love he bears for her is strong, as is hers for him. Their relationship is an incredibly important one for the plot of the novel, since the entire adventure is an effort to save Mrs. Vey.
The ties between the members of the Electroclan and the members of Hatch's twisted operation resemble between family members as well. The heroes become quite close in the course of the book; Zeus sacrifices himself to save everyone else, and then Jack bravely returns to rescue him. Michael sacrifices himself to save his whole family: his mother, his girlfriend, and all his friends. The Electroclan has become Michael's new family.
Nietzschean Supremacism vs Human Charity
Taken from a philosophical standpoint, the main conflict in the novel concerns the proper use and place of humans with electric powers. Hatch wants them to rule the world, using the "chickens" as playthings and catalysts to greater power, while Michael and his friends want to respect others with kindness and goodwill. The metaphor of the eagles and chickens, espoused by Dr. Hatch, exemplifies this dichotomy; in his view, the eagles are so far above the chickens that they have the right to do anything they want, while in Michael's view, they're all human and deserve to enjoy their freedom and rights.