Belinda and Joe-Joe reluctantly travel to New York for a six-week stay with their adoptive father Greg who is getting remarried. That night Belinda dreams again about a mysterious man whose face she can't see, which recurs in her many drawings. The trip is a disaster and Belinda, angry that Greg wants to take the kids away from Loretta, the only mother they've ever known, reminds Greg that he is not their father.

Before he can drive them home Greg gets a call from the museum where he works. There's been a break-in. While Greg investigates, the kids stumble onto a tiny exhibit called Kush. The Little Old Curator piques Belinda's interest but disappears before she can find out anything more. Soon after, the kids chase a mysterious man out of the exhibit only to lose him in the subway.

Returning to the museum, they sneak back into the exhibit and stumble onto a gateway that transports them back to a beautiful temple in the ancient city of Napata, the capital of Kush. They meet Ib the Phoenician pedaling his new alphabet in the marketplace. When the queen appears with her royal procession, Belinda realizes that the man with her is the one they chased to the subway. Joe-Joe falls asleep and is carried off on a runaway cart. Belinda gives chase; Ib, curious about Belinda's book filled with letters, follows and the trio get lost trying to make their way back to the temple.

In an alley they meet a mysterious Old Crone who mimics the fight Belinda had with Greg and hints that the someone has lost something precious to them, then disappears after showing them the way to the temple. When they arrive they are captured overhearing the high priest Smendes plotting to do away with the queen and hand the kingdom over to the Romans. In trying to escape, Joe-Joe is transported back to the present while the man from the subway, Osorkon rescues Belinda and Ib.

Far outside the city in the desert Osorkon explains that Belinda is in terrible danger. He has been traveling to the modern world in search of the children of the king and queen and believes he's found them: Belinda and Joe-Joe. But now that the Romans are inside the city he must raise an army and protect the city and the queen. Osorkon leaves Belinda with Ib and instructs him to find a way to send Belinda home if he does not return. Riding furiously, he is captured by someone who looks like the queen and awakes to find himself imprisoned by Smendes.

Meanwhile, Joe-Joe returns to find a worried Greg. He explains what's happened and that Belinda's been captured, but when they return to the exhibit it's gone. Loretta arrives and Joe-Joe goes back to the room where the exhibition was. Outside a window he spots the Little Old Curator preparing to leave in an old circus wagon and tries to chase him down. Meanwhile back in the past, Belinda realizes that she's actually overheard a plot to kill the queen and starts back toward the city against Ib's advice. They are met by the mysterious Old Crone who reveals that in fact Belinda and Joe-Joe are the lost children of the queen and that the queen actually knew that the Old Crone had taken them in order to protect them from the high priest.

Hurt by the thought that her mother willingly gave her up, Belinda briefly decides to return to the present, but when she realizes that Greg and Loretta are getting on with their lives she decides to return to help the queen and her adoptive parents watch astonished as the kids disappear in the Old Curator's wagon. Returning to Kush, the kids arrive as the Romans have brought a magic sarcophagus as a gift for the queen who invites them, for hospitality's sake, to eat before they return to Rome. Ib helps Belinda and Joe-Joe sneak into the castle, but they are caught and brought before the queen. Belinda reveals Smendes' plot, and a fight breaks out between the Kushites and Romans.

Smendes, whose intention has been to take over both Rome and Kush uses his magic amulet to attack both sides when the Roman General kidnaps the queen. Belinda and Joe-Joe free the queen and Osorkon and all rush back to the main hall where the Romans have been captured. Smendes finally discovers that Belinda is the queen's daughter and tries to throw her from the roof, but Belinda grabs his amulet and drops it, destroying it and him. The queen is desperately grateful to be reunited with her children and promises never to let them go and the Old Curator happily disappears into the ether, having set things right for the time being.