I think what he was expecting after a not having seen the show since he was 3 years old was a plot where Clayface wants to do something bad and Batman has to stop him.  Instead, this is what he got:

Lucius Fox, an employee of Wayne Enterprises, goes to meet Bruce Wayne in the middle of the night in an abandoned tramway station.  Lucius, it seems, has some information on a crooked industrialist named Daggett that he’s turning over to Bruce so that Bruce can give it to the district attorney (which would be Harvey Dent, but that’s another story).  Bruce Wayne, however, turns out not to be Bruce Wayne but rather an actor impersonating Bruce Wayne, on the behalf of some gangsters working for this Daggett fellow, who want Lucius dead.  This actor turns out to be a Lon-Chaney-style “Man of 1000 Faces” named Matt Hagen.  Hagen was in an accident years earlier and sold his soul to this Daggett creep in exchange for a miraculous makeup compound that gives Hagen the ability to fix his scarred face enough to keep working in movies.  Trouble is, the makeup is addictive and makes your skin fall apart if you stop using it (a plot that WB would use again, to little effect, in their movie Catwoman, which might as well not have been based on a comic book at all for all it resembled the DC character).  Meanwhile, Daggett has gotten tired of Hagen’s unpredictability and puts a hit on him.  Daggett’s hit men could easily shoot Hagen, but they decide at the last minute to, instead, dump a beaker full of this magic makeup gunk on his face.  The gunk soaks into his skin and affects him on a cellular level, turning Hagen into the hideous Clayface, a monster with the ability to mold his features into any form.

And that’s just Part One.

Setting aside thedarkness of tone and the ugly, brutal quality of the violence, Sam was utterly baffled as to what was going on.  As well he might be.  He kept turning to me and saying “What’s going on?  Where’s Clayface?”  (Clayface, indeed, does not even put in an appearance until well into Part Two.)  Once Clayface appeared and Batman started pursuing him, he was still confused.  “Wait, why is Batman after Clayface?  What did Clayface do to Batman?”  (Imagine: he’s five years old, yet he already grasps the notion of “probable cause.”  A costumed vigilante can’t just pursue a shape-shifting monster merely on a hunch, there are rules!)  I tried to explain as simply as I could what was going on, how Batman (that is, Bruce Wayne) isn’t after Clayface per se, he’s after whoever tried to kill Lucius Fox, and that leads him to Hagen (but not before a couple of dead-ends and having to spend the night in jail), and Hagen, after a great deal of angst, embraces his new-found powers as Clayface and uses them, not to commit crimes, but to get even with Daggett, the corrupt industrialist who made him this way.  So Batman, by the end of the show, isn’t even fighting Clayface, but trying to help him reintegrate his fractured personality, an issue close to the heart of the 1992 Batman.

It’s impressive how much these early episodes of Batman TAS were real detective shows; there are gangsters and murderers and briefcases full of incriminating evidence and surprising amount of innuendo, references to things unsaid and shady, mysterious moral zones.  Characters sometimes have complex, perverse or contridictory motives; you have to really pay attention to follow the plot, even as an adult.  Also impressive, after watching so much Justice League, is how dark and painterly the animation is (that is to say, it looks like the Fleischer Superman shorts).  Justice League looks like a kids’ show in comparison. 

But the darkness and complexity of the plot was a little too much for my little guy to soak in and he needed a pallette-cleanser.  He chose “Beware the Grey Ghost,” an episode where Batman teams up with the actor who used to play Bruce Wayne’s favorite costumed crime-fighter, the Grey Ghost, to solve a series of mysterious Grey-Ghost-inspired bombings taking place in Gotham.

This, especially after the scary, sophisticated Clayface two-parter, was right up Sam’s alley.  Bruce Wayne watched superhero shows with his dad when he was a kid!  Sam was right there.  He completely understood who the Grey Ghost was and what he meant to Batman, and it was revealed that Batman has a secret cache of Grey Ghost toys and action figures, you could see the Batman universe snap into sharp focus for him.  And when Batman teams up with his childhood hero in order to solve a crime, it was wish-fulfillment on a meta-level. 

For Sam’s 45-year-old dad, there was great humor in the episode as well, since Adam West voiced the part of the Grey Ghost and the mad bomber turned out to be a demented toy-collecting manchild played, both in looks and voice, by series producer Bruce W. Timm.

For a bedtime story, it was the new issue of Justice League Unlimited, where B’wana Beast saves the day by punching a giant bee.  That was one he could easily wrap his mind around.