The villain nearly kills the hero the first time they fight but in the second meeting, the villain is killed almost immediately.
The villain starts out being the main issue of the show, even episodes that didn't focus on him personally ended up being part of the plot to destroy him or part of his plans. In later episiodes, he's no longer the only villain and preparation to defeat him takes a lot less.
The villain started off being on mostly equal terms with the hero, beaitng him after a hard fight. In the second fight, they ended up stalemating with no winner. The third time, the hero barely pulls out a win.
The heroes get stronger and figure out more of the villain's weaknesses, giving them a better advantage.
The villain may have had a narrow failure after sending most of the rebellion into comas or the morgue, but doing so ended up inflicting critical injuries to him and draining most of his resources, with any followers he may have had now dead, defecting, doing a Mook-Face Turn or simply in jail. He's going to go down a lot easier this time around.
The Villain was going after the heroes instead of actually training and no longer learns new skills.