what if baldino had already made an energy contraption machine, but this one was so strong that it pushed all the energy to the surface and with that it became living itself. This Super Contraption machine could be the final boss.
the story will be something like this:
For some reason, Twinsen's planet's magical energy has been pushed to the surface, breathing life into everything (hence the plant enemies etc), after learning this, Twinsen sets off to visit his good friend and inventor Baldino to see if there's something he can do. There he finds out that Baldino can help, because he knows what's causing the energy movement: his own far too powerful ECM (Energy Contraption Machine). Then Baldino makes a second version of the ECM, which is less powerful, for Twinsen. With this little tool, Twinsen can gather the magical energy, and defeat the Super ECM. When this Super ECM is destroyed all of the Magical Energy will be released and the planet will be saved.
EDIT:
Another possible story:
After electrocuting Frunfrock, Frunfrock became a soul, one of the Sendells of the planet Twinsun. But Frunfrock is still active as a Sendell, with his power he pushed all the energy towards the surface and to itself. Because of this Frunfrock became living again and still wants to rule over Twinsun.
After learning that his worlds energy has been moved, Twinsen sets off to visit his good friend and inventor Baldino to see if there's something he can do. Baldino makes a contraption that absorbs the energy dispelled when Twinsen defeats an enemy into Twinsen's body.