The League investigates John's case in the second chapter. And, big surprise, it turns out John's innocent after all. Ajuris 4 is actually fine, Kanjar-Ro is a liar, and the incident was all a ruse by the Manhunters. Like all sentient robots, the Manhunters have turned on their masters. In this case, it's the Guardians of the Universe from the planet Oa. Comics fans also know them as creators of the Green Lantern Corps.
The climax has John Stewart absorbing the central battery of Oa, as a Manhunter attempts to steal the power for himself. The Manhunters are defeated, John's reputation is restored, and the Green Lantern Corps once again accepts him as one of their own.
Written by Stan Berkowitz and directed by Butch Lukic, "In Blackest Night" is in the hands of a solid creative team. Both Berkowitz and Lukic will go on to create some of the finest moments in the DCAU canon. "In Blackest Night," unfortunately, isn't one of them. The central plot sounds like a fantastic John Stewart story, and there are numerous quick scenes with the cast that hint at the more complex character work to come. (Hawkgirl accidentally refers to Superman as a human. She tries to apologize; he views it as a compliment. This isn't even a Superman episode, but that brief scene sums up the character perfectly.)
As a character piece on John Stewart, however, the story has problems. We're supposed to look back on the opening in a new light, after the big revelation is made in Part One's conclusion. And, yes, you could argue that John is a bit melancholy during that trip to his old neighborhood. But does he seem like someone carrying an overbearing amount of guilt? Did he read as someone with literally billions of souls on his conscience, hanging around the barber shop and shooting hoops?
Contrasting John's humble roots with the grandeur of his new life as an intergalactic cop is classic character building. In this instance, though, it feels shallow. And, later, when the shocking allegation against John is confirmed, he's given precious little to do. He stoically accepts his fate, while the team runs off and gets into adventures, clearing his name. The finale does finally give John some life, allowing actor Phil LaMarr to deliver one of the finest Lantern Oath readings you're ever going to hear, but the wait is irritating. For a story centering on the Worst Possible Thing that could ever happen to John, he's surprisingly absent for most of it.
The earlier Justice League episodes also had issues with the series' visuals, which stunned DCAU fans at the time. Batman: The Animated Series, Superman: The Animated Series, and Batman Beyond were landmark cartoons. Network animation simply was not on this level before Bruce Timm and company reinvented the action cartoon. Initially, however, Justice League lacked this visual appeal. Technical issues caused the colors to air too bright, and some of the design choices just seemed questionable. Those squat, boxy Manhunters, for example, look like someone on DeviantArt doing a bad Timm impression. And the choice to render the Ajuris 5 tribunal as digital paintings, with literally no animation? C'mon. Of course that was going to look cheap.