Millie was a new employee at the Weather Institute near Fortree City. What Bart and the other scientists at the institute didn't know was that the person they thought was Millie was actually Brodie, an agent from Team Magma who was undercover to steal ancient Pokémon data.
After Brodie escaped with the data, the real Millie showed up at the Institute. At first, everybody was cautious and wondering why Brodie had returned. However, Brock was convinced that it was indeed the real Millie, as he had fallen in love with her, but not Brodie in disguise.
Once they determined that Millie was actually Millie, Bart showed her to a room with hundreds of books in it. He asked her if she would mind inputting all of the data into the computers. Millie smiled and said she didn't mind at all.