At the very beginning, General Skun-ka'pe says "Nice try, Sam and Max, but I am far too powerful to be captured again!" I first figured that was a reference to his previous incarceration in the Penal Zone, but after some wild speculation, it's all there.
I'm thinking that the absolute FINAL showdown of the entire season occurs at the beginning of the first episode. At least I would suspect some final showdown occurs, different from the one at the end of the first episode, that is entirely canon.
Now, this might be me wanting to see Max as a bazooka, but I have three other reasons for suspecting this.
Gordon the Brain, at the beginning, says something like, "If General Skun-ka'pe reaches the Bronx, the planet is doomed!" If I followed my first playthrough correctly, there is nothing said about the Bronx AT ALL.
My second reason is this: Sam already has all his belongings at the beginning. The brain began to die when he had to acquire Sam's belongings for him near the finale. Why wasn't the brain dead by the time he acquired the cards and the rhinoplasty?
If you talk to Max at the beginning, he says "It'll probably make more sense when we see it all in order." This may be a subtle hint.
Anyways, that's just wild speculation, but I can't expect anything less clever or awesome from Telltale.
Who agrees or would like to agree, but cannot?