In fact, “Bounty Lost” solves the whole mystery. We learn that Omega is actually an unmodified clone created from Jango Fett’s DNA — just like Boba Fett! Even her name ties into Jango Fett’s clone son, who was originally designated the code name “Alpha” before the bounty hunter named him. Yes, Omega is sort of Boba Fett’s sister…from a certain point of view.
It’s Tech who reveals the truth to his companions after studying Omega’s DNA more closely: “I further analyzed Omega’s genetic profile and discovered she has pure, first-generation DNA,” he says in the episode. “All clones were created from a host named Jango Fett. While our genetic structure was modified for growth and acceleration and obedience, Omega is a pure genetic replication.”
But what does this all mean?
Earlier episodes allude to the fact that so many generations of clones have been created from Fett’s DNA at this point that the original genetic template has been stretched too thin, resulting in mutations in the line as opposed to 1:1 copies of the Gen 1 clones. The rogue-ish Bad Batch, for example, are the result of these mutations. The Empire see these mutations as diminishing returns, and the fact that the clones are designed to age much faster than natural-born humans mean that this army will soon be obsolete, anyway. As Admiral Tarkin makes clear in the first episode, this is why the Empire is considering doing away with its clone army altogether, instead building a new army of conscripts and volunteers at half the cost.
Kamino prime minister Lama Su doesn’t want to lose the Empire’s business, which is why he’s determined to get Omega back. Since the Kaminoans have lost track of Boba in the years since the Clone Wars started, Omega is the only remaining source of Jango’s original DNA, the key to creating more Gen 1 clones and restoring its line of Jango Fett clones to their purest form. Lama Su believes this will put his cloning facility back in the Empire’s good graces.
This is why he hires bounty hunter Cad Bane to recover “the asset” and bring her back to Kamino so that he can extract a sample of her DNA and terminate her before anyone else discovers the secret of her origin. But chief medical scientist Nala Se, one of the key engineers of the clone army, has other plans. She’s grown close to Omega and wants to protect her, so she hires Fennec Shand to intercept Cad Bane and free Omega.