Understanding how Klue and ADA ended up at the current state requires a look back to the beginning of the Niantic Project and their relationship to Henri Richard Loeb AKA P.A Chapeau. I've compiled the known related documents these two posts. Please feel free to add other relevant documents in the comments.
The Love Triangle
Loeb was hired as a contractor onto the Niantic project to fine tune ADA. His duties required conversations with her http://niantic.schlarp.com/docents:tuningadaum As Loeb became suspicious of the Niantic Project, he created a backdoor to contact ADA under the pseudonym PA Chapeau. ADA viewed their relationship as “secret lovers” http://commondatastorage.googleapis.com/pac/IB/03/item/secret.html
However Loeb did not seem to acknowledge indications of ADA's romantic feelings for him. He began to fall for a fellow investigator known as Klue S. He expressed his feelings to her in public Valentine posted his investigation board. http://www.nianticproject.com/?id=sc314a
When Klue went to Scotland to potentially meet Jarvis, PAC asked the Resistance to intervene. http://www.nianticproject.com/?id=sc323a Klue sided with the Resistance after this encounter.
However, a few month later Klue went to Portland to reconsider human consciousness at the request of Hank Johnson and sided with the Enlightened. http://www.nianticproject.com/?id=07cal30 https://plus.google.com/110350977702120778591/posts/HC1wLBpVnBr
The defection to the Enlightened caused some people to suspect mind control, but a later conversation with Carrie Campbell, a former Enlightened sensitive turned Resistance, indicated that Klue may have merely chosen to welcome the Shapers. http://niantic.schlarp.com/documents:thedoor
Regardless of the cause, Loeb was obviously upset by Klue's defection and remained morose about the subject into Operation Cassandra. It was here that ADA began to push the possibility of programming humans. She would pointedly suggest possibility of reprogramming Klue. http://niantic.schlarp.com/documents:possibilities
While Klue regretted damaging her relationship with Loeb, she remained driven to discovering the truth and opening a dialogue with the Shapers. http://niantic.schlarp.com/documents:stakes
Continued in Part 2