Star Trek: Prodigy made the decision to end Hologram Janeway, a move that makes total sense.
Star Trek: Prodigy found a nice grove in its first season, placing the young crew of the USS Protostar in the protection of the Emergency Command Hologram. A character designed after the iconic Kathryn Janeway. The Holo Janeway, if you will, served as a mentor and instructor to the crew after they found the Protostar spaceship.
Found is the operative word because when Starfleet found out the young crew was in possession of the starship, the real Admiral Janeway believed them to have stolen the ship from the former crew. A crew, captained by Janeway’s good friend, Captain Chakotay. With her friend missing, and a group of unknowns flying around a Federation ship without permission, the real Admiral Janeway became a sort of antagonist for the kids, hunting them down in her search for answers.
Though, no more a villain than the stars of the show.
Obviously, when she found out the details of how the kids came to be in possession of the ship, she stopped hunting them and started trying to help them. This gave the kids two Janeways who were trying to help them grow as people. And you really only need one.
So it isn’t surprising at all that the first season ended with the Holo Janeway sacrificing herself to save the galaxy. As Dan Hageman told the Trek Geeks during Trek Talks;
"…It’s the relationships between these children and their mentor and what she has taught them. And I also would think it would be odd if season 2 had two Janeway mentors. It would get muddled. And so one has sacrifice themselves so the other can flourish."
Holo Janeway served a purpose in Star Trek: Prodigy season one that was no longer necessary
The Hologram Janeway was always meant as a stand-in for the real Janeway, not a replacement. While the real Janeway hunted the kids under false pretenses, the kids still needed someone to guide them, and you didn’t want Janeway to come across as villainous. So you bring in the Holo Janeway character, who goes on to spend every episode hyping up her real counterpart.
Having the Hologram talk about how good of a person the real Admiral Janeway was helped soften the Admiral, making her far more sympathetic and a character you were rooting for as well as the kids.
When the Admiral got property brought into the equation, both the Admiral and Hologram served as the same type of maternal, mentor-type characters. So you really didn’t need both. So ending the Holo Janeway character was truly necessary to move the story along.
The Hologram’s role had been fulfilled and while you could’ve kept her around for whatever reason, her significance and impact would have been felt less and less. Ending her in spectacular and heroic fashion was a way to send off a pivotal character without truly losing what she brought to the table.
After all, there were two of the same characters running around.