Catherine Weaver's Allegiance

One of the bad things about Terminator: The Sarah Connor Chronicles (TSCC) being cancelled was that there were a shit load of questions left unanswered. Now I'm aware some series end on a cliffhanger on purpose (looking at you, Animorphs), but this wasn't the case for TSCC.

One of those unanswered questions was who Catherine Weaver is really loyal to. Now some people may think that she has to be a good guy as the plot twist in the finale points to that. But that's really not the case. There is no clear answer as to whether her ultimate goal is to help John Connor past his usefulness to battle Skynet.

Let's look at what has been shown in the series:

In Weaver's backstory we see that she was going to be asked by John to join the Resistance. She was put in a case to prevent her from escaping. When she was let out by unsuspecting Resistance fighters she didn't show any regret in killing them. So she isn't loyal to the Resistance as a whole.

And why was she put in a case in the first place?

Was it just a test by the Terminators Against Skynet?

Or are the Terminators Against Skynet split into groups themselves? Some having different end goals than others?

Maybe one group of the Terminators Against Skynet decided that the Resistance should have the help of the T-1001 but didn't want to leave it to chance. So they would lock her up in the case and then she'd be let out at a place where it would be either she joins or dies?

When Catherine Weaver is in present day she does seem to relate to humans but also puts John Henry's well being above her 'daughter's'. Near the very end of the finale, Weaver says for James to take care of Savannah but earlier in the series she made a remark that Savannah came second to Henry. So Savannah had only a limited time of being useful before it didn't matter if she died.

From a story Jesse Flores tells Derek Reese in Season 2, it is my headcanon that Weaver rescues Derek at one point and so Derek knows what she is but hasn't told anyone. He hasn't even told Jesse.

So Weaver being a good guy isn't certain. All that is certain is that she's against Skynet which means she may be okay with John dying once he's not useful to her anymore.