Le monde fait face à une nouvelle menace prenant cette fois la forme d'Apep, le dieu égyptien du chaos. Libéré accidentellement de son emprisonnement, ce dernier utilise les personnes qui se trouvent sur son chemin pour faire des ravages. Tandis que les agents de la DOSA font leur possible pour contrecarrer chacun de leurs gestes, les bibliothécaires se démènent pour arrêter Apep. Flynn, obsédé par la capture du dieu égyptien, convainc quant à lui Charlene de revenir contribuer à la cause.

This is the first series to feature Matt Smith as the eleventh incarnation of the Doctor. Karen Gillan is introduced as the Doctor's new companion, Amy Pond. Alex Kingston returns as River Song, a mysterious woman from the Doctor's future who summons him twice. The main story arc concerns a pattern of cracks in the universe that are sometimes unnoticed by the characters. It is discovered that the cracks can erase things from existence.

There's a new drink taking the world by storm — Bubbleshock! Everyone's drinking it. When Maria's dragged along to the factory tour by her new friend, Kelsey — a girl with an opinion on everything — she's plunged into the sinister world of Bubbleshock and the mysterious Mrs Wormwood. There's something terrible behind the hype — something Sarah Jane's interested in too...