OMG! Jon Le Bon's initiation really isn't going as planned. He gets stuck with Agent WXT on the other side of the planet - in a wild and arid continent, far away from civilization. As they try to make their way back to the Agency, they meet some odd characters - including Gerald the Flying Hog and Conrad the Atomic Monkey - who will fill them in on the Agency's mysterious past.

A surprising discovery disrupts the Agency's peace, driving a certain agent to ... resign! Will it be Jon? While Billy is in the midst of planning his wedding, Theodore goes missing and Big Beaver is back with a new diabolical plan, Jon sets in motion a dangerous rescue operation like only he can dream up. Will he save the world from imminent destruction yet again?

The First Continent is in danger. The newly re-elected President Tiberius has come up with a plan to steal the most powerful and dangerous technologies from the Agency. As for Super Agent Jon Le Bon, he has been the victim of an accident in Henry's lab and finds himself shrunk to molecular scale. By chance, he makes friends with a species of nanorobots who live within the walls of Building A...Together, they will try to foil the president's plans.

Now pay attention, because this summary won't be easy to follow! All set? Here goes...The Agency has got its hands on the Intraneuronal 3000, the largest artificial brain ever created. To put the finishing touches on the programming started by Gabriel Lobe, the notorious computer scientist who is still on the run, Billy and Jon have to take a virtual trip aboard the train. To do this, they have to connect their consciousness to the machine and not worry about whether or not things are real...If the adventure were to go wrong, their consciousness would disappear forever.

Life at the Agency is back to normal. Martha hasn't heard from Big Beaver, the agents are dressing up for the Halloween party and WXT is in awe of Agent S. And what about Agent Jon? Oh, right, he's travelling back through time. Back to the Stone Age, over 200,000 years ago, where he talks to the dinosaurs, befriends a strange tribe of blue elephants and tries to find the president's daughter and a mysterious creature called the Entity...

A terrible explosion has left the Agency in ruins. When Jon Le Bon wakes up, he rushes to find Henry, who will help him regain control of the Agency and, if they are lucky, find the survivors of the disaster. Together they unravel the plan orchestrated by Big Beaver and Q. The mission won't be a walk in the park, because an old character is back: Ultra Jon, and he too is determined to rule the world!