In the end, the time machine sort of clashed with Mess' Other Dimension. It happened everytime when father Tokimura was using the machine. Episode 8 had Bun, Sara and a lot of kids trapped in Mess' Dimension -- that's the first time we saw the time machine clashed with Mess' plans, allowing them to escape from the villains.
The Platonium object was needed to make the time machine up and running. Mess tried to steal it from the heroes so that it won't disrupt anymore of their plans.
The early farewell was only for a while as they will return again later. The Tokimura family were the staple civilians in the series.