The Mandalorian season 3 could see the continuation of one of the darkest storylines from Star Wars: The Clone Wars and Star Wars Rebels. The Mandalorian season 2 was packed full of exciting reveals and has set the stage for many new stories to be introduced in future chapters of the show. Luke Skywalker’s dramatic arrival in the season finale, and Grogu’s decision to part ways with Din Djarin, left many fans speculating where the show will go next. However, with the immense popularity of the beloved toddler, it’s clear that Grogu will return. The most likely narrative could conclude one of The Clone Wars and Rebels' most sinister arcs, and finally explain what the Imperial remnants were doing with Baby Yoda in the first place: the revival of Project Harvester.
First appearing in The Clone Wars season 2, episode 1, Project Harvester was revealed to be a plot by Palpatine to kidnap Force-sensitive children prior to becoming Jedi and brainwash them with slave-conditioning protocols similar to the methods employed with clone troopers. Palpatine claimed he foresaw an army of Force-talented spies in his service, “trained in the dark side to peer into every corner of the galaxy from afar.” To carry out this plan, Sidious employed the notorious bounty hunter Cad Bane to steal a Jedi holocron which, when combined with a sacred kyber crystal, would reveal the names of every Force-sensitive child the Jedi had identified thus far. While it originally seemed that this plan was thwarted, with the destruction of Sidious’s lab on Mustafar and the holocron being returned to the Jedi Temple, the Sith Lord did not stop there.
Although Order 66 and the collapse of the Jedi Order resulted in Palpatine’s loss of access to the holocron, his Inquisitors would continue Project Harvester by ruthlessly abducting Force-sensitive children in Star Wars Rebels and transporting them to a secret facility on Arkanis to be forced into serving the Empire. Palpatine’s apparent death in Return of the Jedi seemingly eliminated the need for Force-wielding children to be kidnapped, but The Mandalorian may include the story as part of a new purpose: exploring the efforts to revive Palpatine. Seeing as many elements from both The Clone Wars and Rebels have been brought into live action with The Mandalorian, it’s possible that Jon Favreau and Dave Filoni could be setting up the continuation of the Project Harvester story.
The Mandalorian season 2 contained many references to secret Imperial projects, featuring elements such as Gideon’s Imperial Science Center, technicians that bore the Imperial Department of Military Research insignia, and the revelation that clone engineer Dr. Pershing was experimenting on Grogu's blood. This could indicate that Project Harvester may in fact have evolved into the method that will be used to return Sidious to his former power. Pershing himself explicitly states in his message to Gideon that he was only able to harvest a small amount of Grogu’s high-midichlorian count blood, leading to failed experiments and rejection of the blood from former subjects, which only lends more credence to the theory.
In Star Wars: The Rise of Skywalker, it's hinted (and confirmed by tie-in materials) that the Emperor’s loyal followers utilized cloning techniques to synthesize a new Force-sensitive body for his still-intact soul to inhabit. With the nearly identical vats of mangled Snoke bodies seen both on Exegol and in Pershing’s lab in The Mandalorian, it is not unreasonable to assume that Grogu (and possibly other Force-sensitive children) will be critical to the Empire, and ultimately the Final Order, in their mission to revive their former leader.