Warning: The following contains SPOILERS for Young Justice season 4, episode 10, "Nomed Esir!"
Young Justice may be adapting the miniseries Countdown to Final Crisis (or Countdown), which is considered by many to be the worst Mary Marvel story ever written. This would be a bold step for the animated series, which many DC Comics fans feel has done a masterful job of distilling the long history of the DC Universe into a single shared reality. It would also be an unusual one, as Young Justice has primarily focused on adapting beloved comic book crossovers. Few fans have anything nice to say about Countdown.
Young Justice season 4, episode 9, " Odnu!" introduced the Earth-16 incarnation of Mary Bromfield (aka Sergeant Marvel or Mary Marvel) as one of Zatanna's apprentices. The episode revealed little of Mary's background, beyond some joking references to the Captain Marvel/Shazam name controversy and Mary's inability to say her own code name without losing her powers. It was established, however, that Mary had begun studying with Zatanna to access her magical powers as spells rather than by flying around or throwing lightning bolts.
The precise reasons for why Mary was trying to find a new way to use her powers also went unexplained, beyond Mary whispering to herself that she "had to give it up" because she was too young to handle such power, when asked by another apprentice about her time as a superhero. This seemed to suggest that Mary was corrupted by her powers at some point in the past. This sounds suspiciously like a reference to the Countdown storyline, which featured Mary Marvel's turning to the dark side as a major subplot.
Mary originally lost her powers during the Day of Vengeance event that led into Countdown, where Mary was given the powers of Shazam's archenemy Black Adam. The villain's power corrupted Mary, despite Black Adam having previously been depicted as an anti-hero who drew upon the same magical power source that Mary had. Countdown also contradicted the idea that Mary and her superhero identity were two separate beings, who traded places when Mary said "Shazam!" This idea was teased in Young Justice season 4, episode 10, "Nomed Esir!," when the Demon Etrigan said it sensed "an other" hiding within Mary Bromfield.
These continuity problems soured Mary Marvel fans on Countdown, even before its main plot found Mary abandoning Black Adam's powers, only for her to suddenly agree to become a servant of Darkseid. This occurred for no readily apparent reason other than writer Grant Morrison wanting an evil version of Mary Bromfield/Mary Marvel in Final Crisis. Coupled with a series of increasingly skimpy costumes, fans of Mary Marvel (who had previously been defined by her innocence) found little to like about Countdown or Final Crisis. This makes it incredibly strange that Young Justice would tease the idea of a corrupted Mary Marvel on Earth-16.