I have always thought that despite The Doctor's arrogant, pompous and inflated personality he also has a streak of Kindness and professionalism. His pomposity is the side he manages to exude to the Crew, but when it comes down to One-On-One, he has always kept Doctor- Patient Confidentiality in Highest Regard, even if it is not a Medical "Secret".
So when Seven-of-Nine (And I will not add 'Sixty' this time) goes off on her own and starts her personal study of Intimacy with her fantasy Chakotay, The Doc keeps her secret.
When this episode starts out, we actually are fooled into thinking that Seven really had her Huge Borg Implants removed, and is donning a Starfleet Uniform (Which she looks great in) and is interacting with The Crew, becoming more Hooman than we have ever seen, even to the point of getting Crew Quarters and installing a Baby Grand Piano.
Unfortunately, it's a house of cards, just like her paranoid delusions in "The Voyager Conspiracy", but it is a house of cards that is the result of her Cortical Array breaking down, just like when she downloaded too much Data into her Brain.
And Janeway as well as The Doctor actually encourage her do go on these explorations, but it is just that her timing is off by a few nanoseconds, when she should be trying to figure out a dangerous Anomaly she is playing Chopin Chopsticks with Chakotay while eating Roast Chicken and teaching him the proper way to slice Carrots.
Meanwhile, huge explosions are randomly showing up all around Voyager, they have accidentally strayed in to a Live Fire Testing ground for Alien Smart Bombs.
And in the midst of this, Seven breaks Down. The Doc sees exactly what she is up to, and not one word of this leaks out of his Program.
It seems that The Borg have built in a self destruct for any Drone that becomes too much of an Individual, it's part of her main Cortical Node.
So we have to have a tacit Pause at the Coda, to be continued at some time before the Series ends. Her Holo-Chakotay was simply an experimental choice, but we see that Chakotay might really have a true interest and attraction to her. I've always agreed with this, even more than Tom and B'Elanna. Because if feels natural.
The main thing is that Seven has gone beyond her need for being nursed through these steps toward individuality by The Doctor, she instigated this all by herself.
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