A princess runs to her father's room in a castle in a panic. She arrives finds a man standing over her dead father's body. The man disappears in a ball of light.

Elsewhere, a boy called Max from the town of Palm Brinks attends a circus. By coincidence he overhears a conversation where ringmaster Flotsam pressures the town mayor Need; to find a special stone located in the town. Max makes a loud noise and unintentionally gets Flotsam's attention - who notices Max is wearing the special stone as a pendant. Max escapes, and embarks on an adventure by leaving the town via the sewers.

After leaving the town, Max is told that 15 years ago Emperor Griffon destroyed the world but spared Palm Brinks because he wanted a special stone - Max's pendant - and that Flotsam is one of Griffon's henchman. Flotsam again finds Max but is interrupted and defeated by the princess, who we learn is called Monica. Monica lives in the time 100 years after Max's present. Like Max, she has a special stone. Their two stones - called atlamillia - allow them to travel between Max's time and Monica's time.

Max and Monica use their new ability to time travel, as well as the reopening of the railroad by Mayor Need to go on a mission rebuilding areas of the world that Griffon destroyed. In doing so, they fix the future - Monica's time - allowing them to get the help from the future they need to beat Griffon.

During these adventures, they learn that Emperor Griffon possesses a gold atlamillia - the most powerful of the three - but desires the other two to make him all powerful. Upon Paznos's completion, Max and Monica use it to help defeat Griffon's army in Monica's time. During the battle, Max and Monica receive word that Ixion has also been completed at Luna Lab.

Max and Monica use Ixion to head 10,000 years into the past to face Emperor Griffon, a young moon-person who lives in Moon Flower Palace. He tricks them into thinking they had defeated him; stealing their atlamillia and reveals his real form. Griffon plans to summon the Star of Oblivion, which will destroy all life on Earth and allow a new, better world to grow in its place. He starts by moving his palace into the sky of Max's time to destroy the world.

Max and Monica return to Max's time with Ixion, and travel to Kazarov Stonehenge - a place that can act as a time portal - allowing them to bring Paznos to Max's time. They activate it, and Paznos arrives in Max's time and sends the Moon Flower Palace crashing to the ground.

Once again, Max and Monica face Griffon at the Palace. They instead meet a woman named Alexandra, who tells them she owns the Palace and that Griffon was once an orphan child called Sirus, whom Alexandra adopted. Sirus has forgotten his childhood because of the evil inside him. Alexandra asks them to restore the palace's garden to remind Sirus of his old life.