As a Captain of a Zero Squad

Zero shows obvious favoritism for Kallen, for many reasons, she is the first one to trust him and he knows her more personally than the others, she keeps his identity secret, she's his ace, and so on. Kallen's first suspicions about Zero occurred when he had her under his geass, and wasted it to find out who she really is, and then couldn't explain how he knew about Shinjuku when he mentioned, trying to use his geass on her a second time. She believes Lelouch is Zero, which is true, but is thrown off his path when he has "Zero" call her on the school phone while he's in the room with her (it was a pre-recorded message).

Zero was responsible for Kallen's understanding of her mother. She would have never known about her mother's refrain use, or why she really stayed as a maid if the Black Knights weren't sent to raid the facility. Because of that event, Kallen is given another reason to fight. Zero soon after calls Kallen his ace and gives her the Guren. Kallen chooses to follow Zero to the end. Why? She realizes that Zero isn't using the Guren to protect himself while the Knights are sent in sub-par models but is using his facilities for the end goal. Kallen also sees him as their only chance. They weren't able to stand a chance against Britannia if Lelouch hadn't come along. She claims they don't need to know because Zero's only ever helped them. Zero seems grateful for Kallen's help. In the end though, Kallen is the only one to find out Zero's identity when she, as Captain of the Zero Squad, goes after him to stop Suzaku. Kallen sees that Lelouch is really Zero and feels betrayed. She always knew Zero was Britannian but to find out that Zero was a boy, her class mate, who would treat life as a game, and would go so far as to take over their school and make it a base during the Black Rebellion, nearly destroys her will. Kallen begins to think Zero may have been only using them for his own amusement.

Although Kallen joins the mission to get Lelouch's memories back, she makes a point of letting Lelouch know that she isn't going to follow his orders, or even trust him, that she'll only listen to Zero. She wants to ensure that Lelouch never controlled her with Geass at any point during the time they spent within the Black Knights. She's slightly disappointed because she finds herself unable to accept Lelouch as being Zero.