Sometime before, Zatanna was contacted by Alfred Pennyworth for help in hiding the crippled Bruce Wayne from Superman and his forces. Zatanna then moved both Alfred and Bruce into the Tower of Fate, well outside of any dimension Superman would be able to reach.
In chapter two of Year Two, Bruce awakens and is greeted by Alfred and Zatanna, with the magician explaining where he is and assuring him he is safe. When Bruce attempts to get up, Zatanna uses her magic to put him back to sleep.
In chapter four, Zatanna is present along with Doctor Fate when Bruce regains consciousness just as his cellphone goes off with a call from the President. When Bruce asks if the Tower of Fate gets cellphone reception, the Doctor cryptically replies, "We are in all places and none." before walking away, with Zatanna jokingly explaining, "I think that's Doctor Fate's way of saying, "Yes, it gets cell phone reception"."
After a long absence, Zatanna reappears in chapter sixteen, the day before the war between the resistance and Green Lanterns against Superman's forces and the Sinestro Corps. Zatanna teleports to Oracle's secret base, informing her and Black Canary, "It's time." She then teleports herself and Black Canary back to the Tower of Fate, where she hears the tail-end of Batman and Catwoman's argument over how Batman knocked her unconscious instead of accepting her help against Superman.
"She gets to hold that against you forever." Zatanna tells the Dark Knight with a smirk as she adjusts her hat. Batman then asks her if she could help heal his back faster, and while Zatanna says she could, she informs Bruce that if something were to happen to her that would cause her to lose focus or something else caused her to break the spell, Bruce would find himself "Bat-floored".
Zatanna is present as Batman delivers a speech concerning the imminent war against Superman, before she teleports Alfred, Catwoman and Black Canary, who gives Zatanna her newborn son Connor to protect, to the Batcave. Batman then tells Zatanna not to get involved if something 'unthinkable' happens, saying they will need her for 'Plan B', before telling her to teleport him to Oracle. Though Zatanna reminds him that their friends think he's staying in the Tower of Fate where he's safe, Batman insists he has to make sure Superman goes down.
Though not witnessed, Zatanna teleports Batman to Oracle.
Zatanna's final appearance in Year Two is a brief scene in chapter twenty-four, standing close to Doctor Fate while holding the infant Connor Lance in her arms.
Zatanna returns in the first chapter of Injustice Year Three. Zatanna is present alongside Doctor Fate in the Tower of Fate when the doctor alerts Zatanna that something is coming. Zatanna is shocked, thinking it is impossible for something to reach them while they are outside of time and space. Doctor Fate tells her to be ready as he prepares some spells while Zatanna hesitantly approaches the tower's doors as something raps on them.
When Zatanna opens the doors, she is shocked to see John Constantine and a young girl standing outside in oblivion, the British mage greeting a shocked Zatanna before asking to be let inside, citing that oblivion is 'chilly'.
Sometime later, Zatanna is shocked to learn that the girl is John's daughter, Rose, and Constantine requests for her to watch Rose for a bit. When Zatanna asks why and where John is going, Constantine explains that something was observing him in Liverpool, with Fate confirming this as well, both sorcerers having felt a powerful presence. Constantine then asks Zatanna to send him to someone, and when Zatanna asks who, Constantine replies that she already knows who.
Zatanna tells Constantine, "He's hiding. After everything that's happened..." as well as telling Constantine, "He doesn't like you." After Constantine pleads with Zatanna, she agrees to send him to see the greatest detective in the world.
In the second chapter of Year Three, Zatanna is in contact with Batman as the Dark Knight questions her on whether or not Constantine is coming to their meeting spot. From the Tower of Fate, Zatanna reassures Batman that he will, though admits that Constantine isn't known for being punctual.
In the third chapter, Zatanna gets Harley Quinn from the Flash's cell, informing her that it's time for them to go. Zatanna then teleports them both to the home of Jason Blood, where Harley first sees John Constantine. Zatanna warns Harley that Constantine is dangerous, though this just intrigues her more. Zatanna is silent throughout the Insurgency's meeting until the Spectre suddenly attacks, resulting in Jason Blood and Harvey Bullock's deaths.
In the next chapter, Zatanna casts a protection spell to fend of the Spectre's assault, though her power is barely enough to keep the Spirit of Vengeance back and she cannot teleport the group away and maintain her protection spell at the same time. Batman decides to confront the Spectre himself and orders Zatanna to teleport the group away when she feels the spirit cease his attack. Zatanna does as the Dark Knight orders, and teleports the group back to the Tower of Fate but not before promising both Klarion the Witch Boy and Catwoman that she would save Teekl and Batman.
Zatanna then teleports next to Batman as the Dark Knight is held in the grip of the Spectre, snatching Teekl by his neck and grabbing Bruce by his shoulder before teleporting them back to the Tower as well.
In chapter five, Zatanna works alongside Harley Quinn and Alfred to keep Detective Chimp alive from his injuries received from the Spectre, with Zatanna revealing her magic is the only reason the chimp's heart is even still beating. Zatanna is quiet when Rose Constantine wanders down and Doctor Fate arrives to usher her away after a heated exchange with Harley Quinn.