In Bucky's room there's a toy airplane with A113 emblazoned on the side - an Easter egg referencing the California Institute of the Arts.
Zeta continues his search for Eli Selig, kicked off in His Maker's Name (2001) when Nelson Arroyo gave the synthoid the name of Project Zeta's lead scientist.
After Zee mimics Bucky's voice, Ro panicked and reminds him of the conversation they had when he did that to her in The Accomplice (2001).
During the analysis of security footage, Bucky checks footage from the Sorben Institute against footage from Zee's visit to Dyron Aerospace, which was seen in His Maker's Name (2001).
When Bucky inspects Zeta, comes to find all of his weapons are missing. This is because the synthoid threw them out in his debut appearance in the DCAU, the Batman Beyond (1999) episode Zeta (2000).