Hanna/WMG

Sophie's little brother was another one of the super-soldier kids

He is very calm through the whole movie, and very observant, easily spotting Hanna in her hiding place but doing nothing to indicate shock or to blow her cover. Later, he wordlessly helps her sneak out of the van without drawing attention from his parents.

Marissa is actually Hanna's dad.

Our introduction to her goon squad takes place in a transexual stripclub with several choice bits about the owner's preferences for, ah, performers. Here's a hint: He likes them with 'parts' from both men and women.
Listen to the way Marissa laughs when she reveals that Erik is not Hanna's biological father.
Tack on the genuine-seeming parental concern/pride when she listens to and discusses how Hanna turned out, and the parental authority when Hanna tries to walk away.
- The problem with this theory is that, after she confronts him about not being her father, Erik outright tells Hanna he recruited her mother (Johanna Zadeck) at an abortion clinic. This implies he was hired to persuade already pregnant women to join the CIA program (likely under some cover story) rather than give up their unwanted children.

== Marissa actually did have a genetically-enhanced baby of her own like Hanna, whom she had to kill. == This moment was her Moral Event Horizon, and she therefore sees Hanna as the daughter she could have had. The last two points in the previous theory about Marissa being Hanna's transsexual father support this theory also, while alternately, many of the points listed below can also support that theory too. At any rate, it's at least implied that Marissa was indeed a parent at one point, or sees herself as one.

Look how distraught Marissa gets when she listens to Johanna's tapes about the joys of pregnancy and later, when Hanna's grandmother says that anyone without children wouldn't understand the loss of a daughter, Marissa becomes so upset she shoots her in the head.
In the flashback when Marissa is about to kill Johanna, Johanna looks up at Marissa and says, "She can never be yours." This could be interpreted to mean Marissa had her own child.
When Isaacs asks Marissa if she has children, Marissa responds that she "made certain choices," an ambiguous statement, rather than directly answering.

Marissa and Erik at one point were lovers.

What with how obsessed Marissa is about being the one to personally kill Erik, despite her department's increasing annoyance, and their sexually-charged phone conversation.

Hanna is the clone Hannalore from Questionable Content theorized she might have.

There's a physical resemblance but Hanna must have been made after Hanners to account for the age differences. This also explains the similarity of their names, as it would be confusing to have two clones with nearly the same name, but Hanna was clearly named after Hannalore. Hanners' mom and dad are Hanna's parents and the woman Erik considers to be Hanna's mother is just a surrogate, hence Marissa's laugh at the question of Hanna's parentage: not only do they not know who the father is, they don't even really know who the mother is.

Hanna is one of the clones created by Franchise.

She's practically an albino in this. Given that she's the sole survivor of a cancelled project, the Franchise presumably used different cloning methods after her.