The Illusion of Safety
Much of the novel is concerned with the Electroclan resting and biding its time in places that are considered "safe" from Elgen threats. These locations serve as safe havens from which to operate and enact their plans against Dr. Hatch and his cronies. All these "safe" places, however, are proven to be ineffective and unsafe: the hotel they're occupying in Taiwan is overrun by Elgen, and everyone is captured. Even Timepiece Ranch, the base of the Resistance, is found and destroyed by the Elgen. Safety appears to simply be an illusion in this installment of the series.
Reunion
Reunion is a major theme of the novel as well. People who have been separated for a long time are suddenly reunited, forming a bond of affection and connection in anticipation of the storm to follow. For example, Michael's mother and Ostin's parents are at the ranch when they arrive, leading to warm welcomes. Taylor's mother even shows up later, having been flown in without her knowledge, and quite a few tears of joy are shed. Tessa and Grace also reunite, having been friends years ago when they were both under the control of Hatch. Near the end of the novel, the Electroclan also reconnects with Tessa and Zeus.
Race for Power
In the battle between the Electroclan and the Elgen, each side is advancing in its power, trying to gain an edge over the other to subdue it. The members of the Electroclan are growing more powerful, training with Gervaso and discovering new things about their powers. Michael, for instance, realizes that he can stop bullets.
Dr. Hatch is taking an even more aggressive approach to growing stronger. He kidnaps Jade Dragon, a young Chinese scientific and mathematical prodigy, in order to gain the power to create more electric children. This whole novel is about Hatch's aspirations to power and the Electroclan's attempts to stop him.
Morality vs Amorality
The Electroclan and the Resistance represent a foundation of morality that is attempting to stop the spreading wave of moral anarchy propounded by Dr. Hatch and his philosophy. Hatch believes in the inherent superiority of strength, teaching his electric pupils that the world is simply their playground. Normal humans (or "Nonels", as he calls them) are weak and worthless, and their lives exist merely to advance those of the Glows. This battle between the Electroclan and the Elgen thus represents that of good against evil, each struggling to retain a hold on the divided world.
