WARNING: The following contains spoilers for The Mandalorian.
Now that The Mandalorian has acquired The Child, AKA Baby Yoda, he's expected to return him to the Mysterious Imperial client played by Werner Herzog, but what does the Empire want with Baby Yoda? Episode 3 of The Mandalorian, "The Sin", sees The Mandalorarian, Dyn Jarren, return to his base of operations to collect payment for his bounty, only to have a change of heart.
He was introduced as a cold, calculating, ruthless, and no-nonsense bounty hunter, but the Mandalorian is proving to be anything but. During the scenes of his armor forging, we keep catching glimpses of him caught in a battle as a child while Super Battledroids attack, suggesting there's more under the emotionless helmet than viewers may realize. After Baby Yoda used the Force to rescue him from the mudhorn, Dyn may have begun seeing The Child as more than a simple bounty. After all, as the internet can tell you, Baby Yoda is irresistibly adorable.
When Dyn collects the bounty on The Child, he attempts to ask what they plan to do with it, only to be reminded the Bounty Hunter's code says it's none of his business after he's accepted payment. Dyn moves on, but under the black visor it's apparent he has concern for The Child and feels guilty for just handing it off for who knows what end. After getting a major armor upgrade (and a badass whistling bird upgrade to his gauntlet), The Mandalorian tries to leave, only to find a knob on his ship had been unscrewed in an act that was likely committed by a Force wielding 50-year-old Yoda baby. This pushes him over the edge and he finally circles back to do something to protect The Child.
While scoping out the bunker, Dyn picks up on a conversation where Herzog's character, The Client tells Dr. Pershing to "extract the necessary material and be done with it." Pershing clearly doesn't like this and pushes back, reminding The Client they were "explicitly ordered us to bring it back alive." Clearly sensing time was drawing short, The Clint simply tells Pershing to finish quickly "as I no longer can guarantee your safety."
This raises a number of questions, some of which have already been floating around. Namely, what do they want with Baby Yoda? But now, another mysterious question is who are they really working for? The Client appears to infer they're performing a task for someone else, but Pershing also points out they were instructed to bring The Child back alive. Are they both speaking of the same mysterious force? The logical assumption is they're performing the duty for an Imperial warlord (since The Empire no longer exists).
As far as Baby Yoda goes, Dr. Pershing seems to be the major clue here. It's already been heavily speculated that he has a connection to the cloners on Kamino because of his white and black tunic and the unique patch, only seen on clone cadets in Star Wars: Attack of the Clones and Star Wars: The Clone Wars. If he's connected to the cloners, does that mean Baby Yoda is a clone? Or, are the trying to make a clone of Baby Yoda? Considering The Client ordered Dr. Pershing to "extract the material," something Pershing planned to do without killing The Child, perhaps he was extracting genetic material for the cloning process. However, The Client's instruction to simply "be done with" The Child suggests it's disposable, potentially indicating it is a clone and they believe they can easily replace it.
Unfortunately, the little med bay in which The Mandalorian finds Dr. Pershing and Baby Yoda only has what appears to be some basic monitoring equipment and an interrogation droid, which may have been adapted for medical purposes (the two functions are unfortunately not to dissimilar as far as the droid's equipment is concerned), so it's hard to know what Pershing had planned. Although we're pretty sure it involves cloning.
Regardless, The Mandalorian and Baby Yoda are back together again. After an epic bounty hunter vs Mandalorian showdown, tho duo escapes the planet, likely with a galaxy of bounty hunters on their tail.