The first letter of each episode of Season 3 spells out "PREPARE THE ANTI-LIFE EQUATION".
The gold ring worn by the waitress is a flight ring belonging to a member of the Legion of Super Heroes, a group of super-teens commonly depicted as living 1,000 years ahead of standard DC Comics continuity.
When Superboy supports Black Lightning's claims against Luthor, he also reveals that he is a clone. His clone announcement is the same thing he told Aqualad, and the others in Season 1, episode 2, when the team found him. He adds a few details, that Luthor's DNA was used, and that he was supposed "destroy Superman if he turned from the light - Lex Luthor's light."
Appearances of Arc number: time stamp 16:16 ; date 2-16; mention of Brion being born 16 minutes after Gregor.
The events depicted occur on February 15th through 17th, 20th and 21st, and 23rd through 28th.