Discussion about "Pardoned Pals" Ending

Ok so, this is the ending that I understand the least in The Henry Stickmin Collection (it's not my least favorite one though).

The thing is: At the start of the mission, Henry and Ellie are reaching the secret jungle base to join them, that's basically the whole deal during the mission. However, at the final choice, you can either choose the government or the toppats (both are correct options).

Now... I WOULD kind of understand why Henry would think twice and join Charles, but why exactly Ellie? I mean, it could be because she follows Henry and is up to do what he thinks it's the best, but what would make her suddenly change her mind? Especially if we consider that the PBT path you are still considered a criminal, so you don't really have anything to motivate Ellie to join the "good side", if you get what I mean. Would it be because of the deal about returning the Romanian Ruby?

Talking about it, I just find funny how Henry steals from the Toppats and yet, he wants to join them afterwards. Don't know, it's just a funny contradiction. Maybe that's also mostly because of Ellie.

What are your thoughts about it?