With the revelation of the 100th episode – that Nora has been communicating with Reverse Flash – many theories have come about as to why she may be working with someone who she even mentions as The Flash’s archenemy.

1) Thawne Knows How to Save Barry:

Following in the footsteps of her father Nora could be taking steps to save her parent and if Thawne reveals he knows how to save him, Nora could think the ends (freeing Thawne and ramifications for messing with the timeline) could justify the means (saving her father, a hero).
That being said Nora didn’t realise until the 100th episode just how much Thawne hates Barry and vice versa, and therefore would not think that Thawne may be manipulating her into sealing her father’s future fate because why would he ever want The Flash to come back?
This theory is very obvious and I have to think that The Flash wouldn’t go down such an easy route like this but it would explain why Nora sends Thawne messages about her experiences as a way to make sure she is making the right decisions in the past.

2) Nora Found a Version of Thawne’s Diary:

If Nora is smart enough to know that she shouldn’t trust Reverse Flash maybe she found his diary about his experiences in the past and in return for having him translating it, she will send him updates about her experiences in the past. Even though this seems like a low-risk trade, Thawne probably uses the information she gives him for some reason and although she thinks she can handle him, there is a reason that even though there were many attempts to end Thawne, he is still running around.
Thawne is the ultimate manipulator and if Nora does not get that from his diary then maybe he planted it to use her.
This theory could actually help Team Flash save Barry in the future cause if they get their hands on a timeline manipulator’s diary like Thawne, they may find a loophole to save Barry.

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3) Nora is Brainwashed:

If Thawne was somehow able to get a hold of Nora and brainwash her into working with him, it could even explain why she may have such a bad relationship with Iris: He could have implanted negative memories with her, that way when she traveled to the past, she didn’t get close to her and reveal anything that a normal mommy-daughter relationship would entail. I mean even the scar that Nora says is where Iris put a chip in her to dampen her powers could have ACTUALLY been a chip implanted by Thawne to control Nora. I mean it could even explain why Nora seems to be having no problem working with Thawne, like it seems she knows that she shouldn’t tell the team but appears to be feeling like she is doing nothing wrong.
This theory could cause a lot of heartaches and may force the team and mostly Barry and Iris to fight their own daughter, this could make for a great finale episode though.

4) Nora is a Villain:

The idea that just because she is Barry and Iris’s daughter, Nora’s automatically good and cannot be a villain is very naive and The Flash has done things where they have a person they trust lie about who they are but what about someone who they love actually be a villain and it has something to do with them. Not like a Savitar situation but more like Darth Vader, where Nora has been drawn to the dark side her whole life, hence her working with Thawne as he is a part of The Legion of Doom and she could be too. It would also make an ominous view about why Nora is here in the past, is she trying to help herself, her father or Thawne?
This theory could go further by explaining that in one version of the timeline Nora turned out to be ruthless villain and so in a desperate moment, Iris gets Cisco or Wally to take her to the past and put the power dampening chip in Nora but now in this timeline, Nora finds the power dampening chip in her and because of that becomes a villain. It is kind of like no matter what kind of parent Iris turned out to be, Nora still was a villain and it might be because of Barry not being around and so maybe the only way of saving Nora from the dark side is to save Barry so that he is around to help guide her in the right direction.

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5) Nora is From an Alternate Timeline:

Nora could be pulling a Savitar here, what if she was in the speedforce when her version of a timeline got changed and then returned to a different version of the timeline, so now to get back to her version she had to get help from Thawne on how to change certain moments in time to get to her timeline version, I don’t know how Cicada fits in it all but I am guessing he might be part of Thawne’s plan to get free or to mess with The Flash.
This theory would explain many things especially why she would not want to tell her parents or Team Flash because it would be like how do they choose one version of their lives over another especially if in the non-Nora timeline Barry and Iris have different children, twins even and the other members of Team Flash have families as well? It would definitely pose a huge ethical question.

6) Nora is Thawne’s Daughter:

6.1) Nora Was Raised by Thawne:
If in the future Barry and Iris definitely have twins, then maybe Nora is the twin that got raised by Thawne to be evil. It would explain why she is working with Thawne and why she doesn’t seem to want to hurt her parents. This storyline is about the same as The Flash villain Cobalt Blue and if Thawne knows everything about The Flash maybe that is where he got the idea from. This would not explain her animosity towards Iris unless she is mad that her parents never rescued her from Thawne and let her be raised by him, kind of like Team Flash could save everyone but her.
This theory could not explain why Nora’s powers were supposedly dampened (maybe Thawne did it himself and Nora is mad that her parents let it happen) and maybe Thawne sent her back to learn from Barry but really just manipulating Nora to mess with Barry because it would hurt them to find out about what happened to one of their kids in the future.

6.2) Nora Was Adopted by The West-Allens:
The West-Allens are known for being generous and taking in a child in need would be very much like them but what if she is the actual daughter of Eobard Thawne and to protect Nora from finding about her true lineage and turning to the dark side, Iris put a power dampening chip in her as well as figure out a way to fool people into believing she is a West-Allen so they don’t judge her and so Nora never tries to have a relationship with her actual father.
This theory would explain how she is a West-Allen but not genetically but was able to pass the DNA test, it would also buy into the story about Nora always feeling different, maybe from her siblings because they had powers and she didn’t (they were just dampened), and then she found out the truth and has built up so much hostility towards Iris for this reason. Nora could be dealing with an inner conflict about listening to the teachings of her one father Barry Allen versus her other father Eobard Thawne causing a deeper Nature Versus Nurture discussion.

All these theories are possible – some more than others – but the ones that tie into the theme of the season, Family Legacy, are the ones that are more possible especially if you consider the Reverse Flash/Thawne family legacy as well.