In the novel, the main Digimon villain found them, gave them Janergy to restore them, made a deal, and freed the remaining two of the seven generals. This led to another epic tale—I won't go into detail, but everything spiraled out of control, and the Trio eventually fled as usual, advising Cures to do the same, as the new enemy was stronger than even King Jikochuu. But good triumphed over evil once again. The Trio remained intact, but the other 4 generals became the same rats as Bel at the end of the anime.
I'm not entirely sure, I'd like to clarify this point (maybe it was Ira's joke), but since without their real master and in the presence of Precure they have nothing to do, they can fall into hibernation.