Book Ends: The pilot began with Jace bumping into Clary, who notices him, and he apallingly asks if he can see her, then in this episode they finally reunite after a year, but Jace tries to evade Clary, who follows him and he asks her the same question in a different tone.
The Bus Came Back: Robert and Max, after the last time they were seen in season 2, witnessing Jonathan's rampage at the Los Angeles Institute. After his death, they attend Magnus and Alec's wedding.
Cruel and Unusual Death: Jonathan kills the Seelie Queen, who can only be heard screaming in pain, probably implying that Jonathan burned her on the spot.
Dead Person Conversation: Clary has one with her mother Jocelyn as a spirit, who warns her against creating runes of her own, which proved to be helpful in previous missions, saying that if she does this again, then she will be stripped of her powers and memories.
Mythology Gag: The Seelie Queen muses that if she and Jonathan were to have a child, their offspring would likely be the most powerful being ever. In the books, they actually had a son together, Ash Morgenstern.
Sadistic Choice: Clary having to choose between using her rune abilities to kill Jonathan, against Jocelyn's warnings, or let him continue his rampage. She chooses the former, effectively fulfilling the promise, but also saving the world.
Sex Montage: The episode's beginning, shortly after the intro, depicts Clary and Jace the Official Couple, Alec and Magnus, as well as the newly minted pairing of Simon and Isabelle (the two beta couples), either having sex or just quietly laying in bed naked.
Clary, after being forced to sacrifice her memories of the Shadow World, resumes her mundane passion of being an artist and becomes famous through her art expositions. Then, she somehow sees Jace, who is glamoured and isn't able to move on from her, and have exactly the same first interaction from the pilot episode.
Simon finishes a graphic novel he's been working on and becomes a Clave Downworlder Deputy.
Alec replaces the late Imogen Herondale as the Clave's Inquisitor.
Isabelle takes over Alec's role as the current head of the New York Institute.
Maia buys the Jade Wolf restaurant and implements a Downworlder equality policy.
Luke becomes a Shadowhunter again and currently works on Clave affairs.
Lorenzo still remains the High Warlock of Brooklyn, but Magnus is appointed as the High Warlock of Alicante.
