The second volume is no more complete in itself than the first one. But it certainly sweeps on with the story and leads to discoveries even before the surprise at the end.
Agatha wakes up. This time not in her father's workshop but in a room she's never seen before. She is, in fact, kept with all the children of nobility and royalty who are called students but are actually hostages. The Baron being convinced that Moloch von Zinzer made the clank, and Agatha would be a hostage for his good behavior, she's there to help Moloch.
What she in fact runs across are a falling machine, Jaegermonsters who think she smells good, an argument about which tropes properly apply, since she isn't the Mad Scientist's Beautiful Daughter ([Spoiler (click to open)]well, actually she is, but we don't learn it here), having tea, carefully hidden teddy bears, and a story about the Heterodyne boys.
In full color, and with flashbacks to Agatha's uncle. By the end of the volume, you can work out why the first volume was so brown.