One storefront in the intro, Food Valley, is seemingly a pun based on the location of Wood Valley. Though, this may have been unintentional as Paul Rivoche's original background labels the store "Wood Valley Shopco".
Zeta's plea to Agent Bennet at the beginning of the episode, that he doesn't want to hurt anyone, is a continuation of the dynamic previously set up between the two in the Batman Beyond (1999) episode Zeta (2000).
As Agent West scans for Zeta in the Wood Valley Bus Terminal, a re-colored Jared Tate model from Batman Beyond (1999) can be seen exiting the vid phone booth next to him.
Agent West is told not to fire his sidearm near civilians and has it taken from him by Bennett. This is in contrast to the Batman Beyond (1999) episode Zeta (2000), where the NSA were fully willing to open fire. This is likely due to the lighter, more kid-friendly tone Kids' WB! mandated for their shows in the wake of the Columbine High School Massacre.