Why was Grogu kidnapped in the first place? As Baby Yoda was whisked away by Luke Skywalker into some kind of Jedi daycare, the question that began the journey of The Mandalorian has still not be answered. Throughout both seasons of Mando, we slowly learned a tiny bit more about Grogu, the Mandalorian sect Din Djarin belongs to, and the overall politics of the post-Return of the Jedi galaxy. However, the plot-point that set everything in motion, has yet to be revealed.
How did Grogu find himself in that strange warehouse on Nevarro, and what did Moff Gideon want with him? Yes, Gideon said outright that it was about harvesting some of Baby Yoda's blood, but to what end?
What was Gideon's plan? Overwhelmingly, the most popular theory to explain Moff Gideon's scheme is that the events of The Mandalorian represent the beginning of Palpatine's infamous resurrection in The Rise of Skywalker. Poe Dameron said "somehow" Palpatine came back, and perhaps the "how" in that statement is that Moff Gideon harvested enough midichlorians from Grogu to get a decent Sith clone body prepared for a reborn version of Palpatine. Presumably, the problem with a regular clone of Palps is that it might lack the necessary midichlorians to sustain all that Dark-Side-of-the Force action. Dr. Pershing often referred to Grogu as "the donor," which means that there is someone who is receiving this blood. The good money seems to be on that someone being Palpatine.
Will Palpatine appear? At the point at which Luke Skywalker appeared in Season 2, and Ahsoka is talking about tracking down Grand Admiral Thrawn, the answer to this question could simply be, "Why not?" If there's a Palpatine clone that lives to "old age" by the time of The Rise of Skywalker, then we could be dealing with a middle-aged Palpatine clone, sitting in a lab somewhere during the events of The Mandalorian. Back before The Rise of Skywalker came out, several fan theories suggested that Matt Smith might be playing a younger-clone of Palpatine in Episode IX. Obviously, that turned out not to be the case. But, the notion of a younger Palpatine in Mandalorian Season 3 is interesting, and, if you look at it a certain way, not entirely unlikely.
What does this mean for Baby Yoda? The fact that there is a Mandalorian Season 3 somewhere on the horizon should make one thing fairly obvious: Baby Yoda and Mando will be reunited. There's no version of Mandalorian Season 3 where Baby Yoda is just not mentioned, and Mando goes about his business a Bounty Hunter or King of Mandalore or whatever. The heart and soul of the show is Mando and Baby Yoda.
So, how could they be reunited? Well, what if Gideon was telling the truth? What if the Imperials did extract all the midichlorians they needed from Grogu? If that's true, could they have actually lowered Grogu's midichlorian count? In other words, was the ability to use the Force effectively stolen from Baby Yoda? If so, you can quickly imagine a reason why Mando and Baby Yoda could get back together. After several months or even a year, new, full-time babysitter Luke Skywalker might notice that Grogu is getting weaker and weaker, mostly because the midichlorians have been extracted. This could then necessitate a new mission for Mando: Find the missing blood!
But, in the meantime, this could also mean that perhaps, Luke might feel like training Grogu doesn't make sense anymore. If you don't have a high midichlorian count, then you can't be a Jedi, right? This is a detail that Star Wars canon has waffled on since 1999. But, if Grogu does lose his ability to use the Force, or even has diminished Force powers, then suddenly there's a very good reason for him to run back to his best dad; Din Djarin.
The Mandalorian Season 3 is expected to debut in 2022.