Well,... not the monsters on Alcatraz.
What was going to happen, if the Elders had their way, was to release the monsters on Alcatraz onto the humans (or humani) on Earth. Then, after a whole bunch of havoc and chaos was created, and the humani had wasted all their weapons and other resources on fighting the monsters (to no avail--the weapons wouldn't be enough to fight the monsters), they were going to step in and defeat all the monsters. Then, the humani would worship them as gods or respect them in other ways, like in the past times. The monsters were to be released by Niccolo Machiavelli and Billy the Kid, and the two were to kill Perenelle Flamel as well. They failed to kill Perenelle, and Quetzalcoatl told them to release the monsters, then kill the Flamels when they came back to Alcatraz to try to stop them.
However, Dr. John Dee has other plans. He was declared utlaga by the Dark Elders, and wants revenge. He wants to awaken the creatures to distract the Dark Elders, and then go back to Danu Talis and defeat the Elders from back in the time of Danu Talis. When Machiavelli and Billy refuse to awaken the monsters, and become waerlogas (warlocks), Dee has to rely on Virginia Dare to awaken the monsters. Black Hawk comes in here, are drives Mars Ultor, Odin, and Hel to Alcatraz to hunt down Dr. John Dee. Dee escapes to Danu Talis with Dare, and Josh and Sophie follow them. After that, we don't know what happens.
And correct me if I'm wrong. I think this is what happened, but I can't be 100% sure.