Grey Griffins: The Clockwork Chronicles: No. 3: Paragon Prison by Derek Benz
In Book 2, The Relic Hunters, the Griffins were on the brink of capturing their enemy, Otto Von Strife, when his portal machine whisked them away to an alternate universe. In Book 3, the children awake to find a world just like theirs. They discover that they have been transported to an alternate reality with some key differences: all the bad things that the Griffins experienced in their own world never happened. This world is near perfect! But the Griffins realize that there's no place like home. They decide to face off with Von Strife in order to find a portal back to their dimension, and, after a battle in which the universe is nearly destroyed, the Griffins declare their final victory and find a way back home.