The guys continue to investigate their "disappearance" by searching the school records, Sam finds clues of his existence from their usual timeline and finds his doppelganger.
The guys are trapped in a storm that leaves strange markings outside their hideout. Felix and Sam go to find protective charms against what caused the freak storm, Andy and Jake try to catch what they think left the markings.
Felix spends time with his younger brother and they are attacked by a swarm of bees, they go to Phoebe to get help from The Book of Shadows, Jake and Andy try to earn some money.
Jake gets arrested by his "dad", Felix continues to read in The Book of Shadows about the elements, Andy is followed by crows, Phoebe shows up to help.
The boys go back to school and try to fit in again but struggle with piecing together old relationships with new ones. However, there's a far more dangerous priority they must deal with as another mysterious force of nature arises.
The boys are suspicious of Pheobe and her involvement in their predicament. Later they figure out what it is that's chasing them and how they might get back to their own time line.
