The following is a list of episode summaries from the Watchmen Animated Series. Those listed that were not aired are referred to by existing scripts and storyboards.

Episode 1: WATCH OUT! Edit

Episode 1 was the pilot episode for the series and as such did (as most cartoons) nothing more than present the settings and characters. The episode starts out with an evil mastermind called "Captain Red" at a base out in some abandoned chemical plant. Captain Red states that the chemicals will allow him to take over America, but he is suddenly shocked as the door blows open and the Watchmen stand waiting. The Watchmen proceed to fight Captain Red's men and show off their powers and abilities. Rorschach is the one to defeat Captain Red as he presses a button and sends the villain hurtling into one of his own chemical vats.

The team then returns to their base to discover that it has apparently been taken over by an evil mummy named Ozymandias. A sleuthing mission begins as they search about various places. Eventually Adrian and Bubastis discover the mummy and proceed to run from it. After some various chase sequences it is revealed that the mummy is Adrian's great ancestor and he has come to warn them about the evil Jack Hackle, an evil god that looks suspiciously like Anubis. The Watchmen then proceed to fight Jack Hackle and save the day. The episode ends with a giant squid cackling maniacally in his base.

Nite Owl Says: The after episode special shows a group of kids near an abandoned factory planning to go inside. Nite Owl and Rorschach arrive to warn the kids how dangerous abandoned buildings can be and how they should never go inside without an adult they trust.

Episode 4: Good Night, OwlEdit

Nite Owl's senile Yiddish father, Hollis Mason comes to visit and he doesn't like how things are different from when he was a Watchman. The episode is a fan favorite for showing a 30 second flashback of the Minutemen when they are stopping a bank robbery. It showed Hooded Justice with an Australian accent which confused fans and had Dollar Bill announce himself as the leader who was more like Captain America. The Comedian was also a member in the flashbacks, but instead of being the same Comedian as in the Watchmen, it was his father, who also makes an appearence by the end of the show to say how proud he is of his son. Tom Hanks guest starred in this episode as the voice of Dollar Bill.

Nite Owl Says: Despite the moral of the episode being about showing respect to your elders, the Nite Owl says segment is different from others. Bubastis is shown alone in a dark room talking about child abuse and how you should tell someone you trust if someone touches you on your private places.

Episode 16: The Black FreighterEdit

Ghost Pirates from the Black Freighter are attacking Manhattan (the island, not the character). This episode is infamous because it was supposedly co-written by Alan Moore himself - in truth, it was co-written by an NYU student named Alan Jacob Moore, no relation to the famed author. Episode 16 did not have a storyboarded Nite Owl Says segment; production notes for what lesson was planned have gone missing in a conspicuous manner, and no one who worked on the show has been willing to mention what it was. Rumors persist that it was a lesson regarding plagiarism in school.

Episode 22: The Comedian's Day Off Edit

One of the few Comedian-centric episodes, the storyline was supposed to involve the Comedian attempting to take a day off at Coney Island, which spun out of control when the amusement park was taken over by the crazy, borscht-loving ghost of Stalin. At least three different versions of this script have surfaced; one had the typical Scooby-Doo ending, with the ghost revealed as a land developer trying to scare people off so that he could buy the property cheap. One ended with the ghost being what it was, and the Comedian's laser being the only device that could harm the undead despot. A third was apparently written during coffee breaks, and was never intended to air, as it ended with the Comedian taking a flamethrower to the entire park, killing everyone inside it. This was confirmed in the July 19, 2003 Watchmen Animated Fan Club chat with scriptwriter Kim Soong Ng, who stated that "Every script got the horrorshow treatment eventually. It was all in questionable fun."

Nite Owl Says: Nite Owl chastizes the Comedian for his atrocious eating habits, suggesting that his teammate try a nice fruit salad or pita pocket instead of a Coney Island dog. The Comedian "compromises", adding sauerkraut, onions, and relish to his dog, resulting in a consternated face-palm by Nite Owl.