They kill the gods offscreen FFS, and it's barely given any thought. Odlly enough, magic still works even though it shouldn't. Main enemy are Necron-esque Wakfu zombies from another dimension that want to eat everything to feed their eternal hunger, look like filler villains to give introduction to a worse villain ala orks, but... They never do. Yugo grows up to young adult size due to a plot convenience. The bad guy from Season 2 is back thanks to the goddes of the Eliatropes, who's now a dirty coward even though the lore says otherwise. The Iop is given even more cocksucking this season, as usual, although he doesn't do much.
Yugo is also given the ultimate power-up (yes, GIVEN, he doesn't earn it, as the bad guy from Season 2 takes the Eliacube, all of the Dofus plus an Elicube mk2 from one Mechanus alien that presumably killed the gods, Yugo does nothing), acquiring the power to destroy the world+2, and when fighting against the main zombie villain (who also has his equivalent of the Dofuses), he only manages to force a draw. But hey, it's not a straight up loss like every previous season at least! There's also an OVA with a cool fight and massive plot-holes, plus a LGTB-shit friendly Eliatrope.