Question about ending [SPOILERS]

Rather than evil I would say that Chigara had an influence in the background affecting how she was behaving, sort of like how when in real life we usually have a 'internal voice of logic' so to speak. While she would have felt she was in complete control and that this logic was her own, the reality was that it was purely artificial and that this influence was giving her a push every now and again in pursuit of bettering their own knowledge and understandings of the galaxy - in the case of Chigara this was the observation of Asaga (as the current Ryuvian Princess).

As the Alpha says in the 2.00 content Kayto entering the picture was pure coincidence and that their growing interest in him would have been on the back of his achievements as captain of the Sunrider, while during the mind stream segment the prototypes claim 'we allowed you free reign in your interactions with him' the reality was that she was never truly free as the conditions for her programming changed were to explore how he could be manipulated. So while Chigara was technically the one becoming closer with the captain it is highly likely that the collective voice of the prototypes were whispering her encouragements that would put her in situations where she could get to learn more about him, for example suggesting the moments for her tea breaks with the captain.

When Chigara connected with the mind stream this would have been the moment of realisation for her, that there was a bigger force at play to her existence and that she goes into denial in order to protect her memories. As a result she finds that she is able to resist the mind stream and ignore her orders to return. Connecting to the mind stream though had one major drawback in which she created a backdoor that Lynn is able to exploit after the defeat of the Nightmare Ascendant leading to the Liberation Day massacre.

By the end of the Liberation Day massacre, Kayto had helped Chigara successfully repel Alice from her body/vessel by strengthening her will power to resist Alice just like Chigara had achieved previously for the Alpha. Tragically though she is shot in the aftermath and like Alice (who has also now lost both her vessels) is forced to return to the mind stream. With two strong wills now residing in the mind stream (Alice and the now fully developed Chigara) the Alpha can no longer or less successfully influence the mind stream herself leaving it corrupted by the conflicting ideology of Chigara (who has become obsessive over the captain) and Alice (wanting to see the destruction of humanity) - the result is a hive mind lets call it a **Ali-gara** that is completely psychotic and unstable. This leads to the prototype lines becoming more disorganised and without one strong voice of leadership they are now acting more independently. This will more than likely change depending on which personality comes through stronger for Chigara/Alice (perhaps high/low affection?) but ultimately will lead to the creation of a new will that becomes the new Chigara completing her transformation to more of an antagonist role (I wouldn't be surprised if that as a representative of this we see Lynn demonstrate split behaviour one moment using Chigara mannerisms to get Kayto's attention and then the next trying to kill him).

Although Return suggesting that the Liberty gets a new pilot strengthens the case that Chigara will no longer be a main girl.