Phineas and Jeffrey help the Wright Brothers invent the airplane and Corporal Eddie Rickenbacker defeat the Red Baron.

Bogg and Jeff land in colonial Massachusetts. Their arrival is witnessed by a local who has them arrested as witches. Benjamin Franklin's mother is also under accusation, and if she dies, history changes. Jeff uses the Omni to prevent him and Bogg from being burned at the stake, but that puts them a couple of centuries forward and right in the middle of a seance being attended by skeptic Harry Houdini. Witnessing the ""supernatural"" with his own eyes, Houdini starts believing in ghosts, further altering history. The Voyagers Omni out, but return when Jeff determines they must convince Houdini they aren't ghosts. He and Bogg end up saving Houdini from being rescued alive, and put that part of history back on track. They then return to Massachusetts with one of Houdini's mirror illusions. Using it, they show that there are no such thing as ghosts and witches: only mechanical trickery. That ends the witch trials, and history is restored.

The Voyagers are separated: Bogg is with Lawrence of Arabia, while Jeff is stranded in the 1800's with Thomas Alva Edison. When Jeffrey awakes after a rough landing, he learns that Edison has dismantled the Omni and not invented the light bulb. A piece of thread is the answer to the incandescent light but Edison can't figure out the Omni. He rebuilds the strange device and Jeff returns to Arabia, unknowingly saving Bogg and Lawrence as they are being led to their deaths. A chase through the catacombs leads Lawrence, Medina, and the Voyagers to safety and Lawrence is reunited with his people. The Voyagers return to Menlo Park to see the electric light used outdoors for the first time.

Jeff and Bogg arrive in 1930's New York and meet a retired adventurer/voyager, Isaac Wolfstein. They drop him off on an island to live out the rest of his life, save Albert Einstein, then pop back to Marco Polo's time...but Polo isn't where he's supposed to be. The two try to restore histroy but Jeffrey is caught by soldiers who plan to sell him as a slave. Bogg goes to Wolfstein to get advice, and just manages to save him from a nuclear test on the island. The two men return to save Jeffrey, then head off to lunch with Einstein.

Phineas and Jeffrey assist a fellow Voyager who is trying to recover the stolen Mona Lisa from a thief aboard the doomed ocean liner Titanic. Then in 1884 France, Jeffrey is bitten by a rabid dog and his only chance of survival is treatment with a new vaccine invented by Louis Pasteur.

Bogg and Jeff land in 1880 London and save famous world-traveller Nellie Bly from Jack the Ripper. The three of them meet with Sir Arthur Conan Doyle, who is suffering from writers' block. Besides making sure Doyle write his Holmes novels and Bly goes on her famous world trip, they discover that Bogg's nemesis, the evil renegade Voyager Drake (from The Trial of Phineas Bogg) is the one who tries to kill Bly as Jack the Ripper.