It's fair to call Star Trek IV: The Voyage Home the most light-hearted of all the films in the franchise. It features the, now, former crew of the Enterprise, going back in time to 1980's San Francisco in an attempt to save the whales. Yup. It's jampacked with some silly but memorable moments like Spock dropping a Bay Area punkard with the Vulcan Nerve Pinch and being met with a round of applause on the bus for doing so.
It's filled with sweet little moments like this, but the biggest and most defining aspect is the crew's quest to save the whales, specifically the humpback whales. It's one of the elements that have defined the series for decades, and now, it's about to share that element with another piece of Star Trek lore.
In recent screenshots for Star Trek: Prodigy season two (obtained by TrekMovie.com), we see what looks to be a humpback whale in some form of container. Rok-Tahk, the young Brikar on the crew, seems to be amazed at the presence of the creator. Not surprising, as humpback whales can be well over 40 feet long in most cases.
They're impressive creatures, so it makes sense that Rok-Tahk would be mesmerized by them. Yet, considering the show's penchant for revisiting abandoned or forgotten ideas every so often, it's far more likely this whale is in trouble and the crew is trying to figure out a way to get it home.
It's also possible that this is a time-travel episode. Considering the second season will have a heavy time-travel element to it, the former crew of the Protostar may be in or around the same era of San Francisco that James T. Kirk, Spock, and the rest of the Enterprise crew were.
If that's the case, that'll set up some interesting plot points to pay attention to. Yet, it's unlikely the show goes that far with this reference. It's far more likely the whale is part of a separate plot, completely independent of The Voyage Home.