Rocky and Bullwinkle reunite with Casper and the Ghostly Trio, together they have to rescue Mr Peabody, Sherman and Dudley Do-Right from the evil warlock and his two henchmen with a help from Casper's witch girlfriend, Wendy and her three aunts.
The evil warlock, Lord Eastputain and his two henchmen, Igor Sikovsko and Mai LingMuno have travelled from the 14th century and the Dark Age. His plan is to capture a talking dog and a boy who has been raised by the dog as a penalty for the use of a time machine. The ripples attract the attention of Wendy and her aunts who are alarmed but don't know why the warlock is here - yet.
In Frostbite Falls, Mr. Peabody, Sherman, Penny Petersen and Dudley Do-Right have come to visit Rocky, Bullwinkle and Karen in the museum. Mr. Peabody starts one of his long winded history lessons - but he is cut off when Eastputain arrives with his henchmen. Annoyed at the interruption, Dudley Do-Right steps in but proceeds to annoy the warlock who decides to kidnap the Mountie along with Mr. Peabody and Sherman. Rocky, Bullwinkle and Karen can't understand how did Eastputain can do a thing like that or why. Penny told the warlock that he'll never get away with this but Eastputain told her that he already had and he and his henchmen disappeared with Mr. Peabody, Sherman and Dudley.
Penny is upset that she'll never seen Sherman again, but Rocky suggests that he, Bullwinkle and Karen go see Casper, Kat, Dr. Harvey and the Ghostly Trio (Stretch, Stinkie and Fatso) in case they can help. Penny agrees and the group make their way back to Whipstaff Manor.
Wendy and her aunts meanwhile are also headed for Whipstaff Manor, suspecting a connection to Desmond Spellman who Casper and Wendy had battled before. They are arrive before the gang from Frostbite Falls and it is quickly established that there is no connection as Eastputain was from the past and Spellman was the present before he was dealt with. Working out what is going on though is proving hard.
Rocky, Bullwinkle, Karen and Penny arrive at Whipstaff Manor, and they meet Casper, Kat, Dr. Harvey and the Ghostly Trio. Penny didn't realize that Rocky, Bullwinkle and Karen are not so scared of ghosts, but Rocky said that evil warlock was known as Sylus Eastputain and he and his partners Igor and Ling-Muno had kidnapped Mr. Peabody, Sherman and Dudley. Casper introduces the gang to Wendy and her aunts, and Gerti has recognised the name of the warlock and is horrified. She quickly fills everyone in and says that it is most likely that he has taken them back in time. Rocky realizes that this may have something to do with Mr Peabody's Wayback Machine, and Gerti agrees. Eastputain hates people who travel in time without his permission.
Meanwhile in the warlocks and witch's lair, the warlock and his henchmen puts Mr. Peabody, Sherman and Dudley inside a cage. Sherman asks Mr. Peabody where are they now, and Mr. Peabody tells him and Dudley that they're in the Dark ages of Highland in 1375. Dudley demands to know why the warlock is doing this, and is told that Mr. Peabody's time machine is interfering with his control of the timelines. Mr. Peabody denies the warlock has any authority and demands their release, but Eastputain laughs this off telling them that he and his henchmen have evil plans for them.
Back in the present, everyone agrees that the only way to effect a rescue is to go back in time themselves. Gerti has reservations knowing they can get into trouble themselves, but Wendy has an extra trick to prevent a ripple in the timeline that the warlock will see. Holding on to each other, Wendy and her aunts combine to send all of them back to 1375. Once there, Wendy and her aunts realize that they can't use their magic to find the warlock as they will give themselves away. They have to look for them manually and to that end the gang splits up. Rocky, Bullwinkle, Casper and the Ghostly Trio head one way while Karen, Penny, Kat, Dr. Harvey, Wendy and her aunts go another way.
Meanwhile in Frostbite Falls in the present day, Boris and Natasha arrive in pursuit of Rocky and Bullwinkle to seek retribution from the loss of their leader's Lazarus machine. They can't find them, but they run into Snidley Whiplash who has arrived looking for Dudley Do-Right. He tells Boris and Natasha he has kidnapped Dudley's girlfriend Nell Fenwick and he was there to show off about it. The Pottsylvanian spies love this act of evil and figure that if Dudley is a friend of Rocky and Bullwinkle he'll bring them with him. So they join forces to follow Whiplash's plans. Their conversation doesn't go unnoticed as Captain Peter Peachfuzz has overheard when arriving for a visit.
Back in 1375, Karen, Penny, Kat, Dr. Harvey, Wendy and her aunts find a castle that they think is Eastputain's lair. But they quickly discover that it has been abandoned. However a number of things have been left behind. Penny finds a diary in some foreign language and Wendy and her aunts have found some old potions. They can't identify the potions without using their own magic, but they are marked in the same language as the diary. Dr Harvey identifies the language as old English, which is unusual as they are in China. Karen's uses her FBI training to try and translate what she can and identifies one potion as a translation potion, but they still need a magic booster. Kat though notices the metallic nature of one of the walls and Dr Harvey realises the metal is lead - which should block Eastputain from detecting their magic.
Taking the punt, the potion is used with a spell from Fanny and now everyone can read the diary. It reveals two things. The first is Eastputain's name is actually Nigel Davis Williamson - explaining the use of old English. The second is that the warlock has put a curse on someone called Lady Julianie putting her in a deep sleep and that he plans to do the same to Mr Peabody, Sherman and anyone associated with them. As they read that two more names appear by magic - Dudley Do-Right and Nell Fenwick. That confuses everyone as Nell had not been kidnapped, until Gerti remembers something else about the warlock. If anyone was close to a person who was a prisoner of Eastputain, if they were in danger that name would be added no matter what. That meant that Nell was in danger back in the 21st century and Dudley was powerless to do anything about it.
Rocky, Bullwinkle, Casper and the Ghostly Trio meanwhile have found the warlock's current lair and have come across the fast asleep Lady Julianie. Not knowing who she was they left her there for the moment, and they find the room where Mr Peabody, Sherman and Dudley are caged. Eastputain and his henchmen are there so they can't move unless they can divert the warlock and his minions. The Ghostly Trio knew scaring wouldn't work so they had to think of something smart. Rocky tells Casper to go and get the others for ideas.
Back at the old castle, Gabby finds a potion that can turn anyone into a terracotta statue - even a warlock or witch. They just need the spell to go with it so a search has begun in the hope that it has been left behind. No one has any luck, when Casper arrives with his news. Karen suggests a distraction rather than a scare and the group follows Casper to the warlock's current lair. All the potions and the diary are brought along.
Once the gang is back together, Karen tells the Ghostly Trio they should turn invisible and make things happen out of nowhere. None of the witches can use their magic to back that up. Bullwinkle wants to use his own magic, but Rocky is quick to reject that reminding him that never worked anyway. Rocky, Casper and Kat would unlock the cage and free Mr Peabody, Sherman and Dudley, while Wendy, her aunts, Karen, Dr Harvey and Penny would seek out the spell. It needed a lot of distractions and a lot of time.
The Ghostly Trio start their spree of mischief. Eastputain is quick to work out that there are ghosts about, but he isn't helped by his henchmen who are scared. Stinkie sees that and wants to take advantage, but Fatso and Stretch tell him to stick to the task as it was the warlock they needed diverted. Eastputain tries a couple of spells but as he can't see the Trio he keeps missing the target. In sheer frustration he chucks a couple of old fashioned whammies, one just missing Stretch by a whisker. Destruction outside the room has an angry Eastputain following the trail with his henchmen, giving Rocky, Casper and Kat the chance to unlock the cage. Casper picks the lock easily.
The distraction is working well, and Penny finds the spell. Casper turns invisible and lets the Ghostly Trio know to bring the villains back. Eastputain and his henchmen return and find the cage empty. Furious, Eastputain waves his hand to reveal any intruders only to hear someone yell "Adharak nirghata zapa cid jagaruka viza!" followed by a puff of purple smoke. When it clears, Eastputain and his henchmen are only half converted. However there is suddenly an explosion of bright yellow light from above - completing the process.
Everyone is stunned, wondering where the yellow light came from. But before anyone can ask any question there is a squeal from a nearby room. It is Lady Julianie who had been awoken when Eastputain had been turned to stone, wanting to know who they were. Rocky fills them in as best he could but only confuses her. Mr Peabody comes to the rescue using his experience in ancient societies to explain things better. Julianie asks to be taken home but no one knows where this is - when suddenly that same yellow light causes a red brick road to appear. The group follow the road that takes Julianie home.
The only issue now is the note that Nell Fenwick may be in danger. Dudley wants to go to her aid immediately but they have to get back to the 21st century first. Wendy and her aunts oblige and they arrive back in Frostbite Falls. Peter Peachfuzz sees them and quickly tells them what has happened to Nell, including how Boris and Natasha are involved. Dudley is about to run off to the rescue, but Rocky and Karen stop him telling him that Wendy and her aunts can get them there much quicker. Another trip courtesy of the witches follows, and they find Snidley Whiplash has Nell Fenwick tied to the train tracks again. Boris and Natasha also have some dynamite set up. Wendy in particular is angry at this sight, and casts a spell that has Snidley wrapped in the rope instead and the dynamite in the pockets of Boris and Natasha, with one stick in Boris' hat. "Raskalnikov! Those pesky friends free Dudley's girlfriend!" They get rid of the dynamite just in time, and Nell runs into Dudley's arms as the train roars by, leaving Boris, Natasha and Snidley coated in black tar from the smoke. The tar and the ropes are quickly scaring right off their bodies when the Ghostly Trio launch a scare and they take off again.
Everyone is relieved. Penny gives Sherman an overdue hug. Everyone wonders out loud who was behind the yellow light that helped them, and over the top of this a mystery voice says - "you will find out - someday". Leaving that behind, everyone goes their separate ways and Rocky leaps to the sky to spell out the words "THE END" before adding "I think!"
- Rocky J. Squirrel
- Bullwinkle J. Moose
- Karen Sympathy
- Mr. Peabody
- Penny Peterson
- Dudley Do-Right
- Nell Fenwick
- Casper the Friendly Ghost
- The Ghostly Trio (Stretch, Stinkie and Fatso)
- Kathleen "Kat" Harvey
- Dr James Harvey
- Wendy the Good Little Witch
- The Witch Sister (Gerti, Gabby and Fanny)
- Lord Sylus Eastputain
- Igor Sikovsko and Mai LingMuno (Lord Eastputain's two goons)
- Boris Badenov
- Natasha Fatale
- Snidely Whiplash
- Peter Peachfuzz
- Lady Julianie