The protagonist has escaped doom... now where does she go?

I see no problem. She goes to the church, but as far as your plot counts, she goes towards... MORE DOOM! That's the only way to write a story until the end.

"Doom, doom, doom, doomy doom, doom!" To paraphrase the great SIR.

If everything is being monitored, don't try to hide. Mislead the watchers; make them guess at where the final destination is--and guess wrong.

Other than that, yeah...doom, doom, doom, and more doom.

"The ships hung in the air in much the same way that bricks don't." --HHGttG
"Does this game have a safe word?" --Rob Balder

That, or she uses the AI to help disguise her. Sure, she's there, but she's actually Jane Smith from the marketing department of MegaCorp. No need to be worried her. Maybe they craft some sort of basic disguise that will help fool the sensors, or give a false impression.

If you're supposed to "write what you know," how does science-fiction or fantasy get written?

What she needs is a good disguise. So even if she gets caught on camera, the watching villains won't know it's her. She could make them think she's some random person, or she could choose a specific person with access to whatever she needs. You can't go wrong with going back to basics.

2008 Winner - Stray Kingdom
2009 - Stray Kingdom 2

Hitch hike to the church with the assistance of some kindly person.

Is said person an agent of the powers pursuing her trying to get information?

Is said person really an innocent bystander who now faces certain doom for getting caught up with the MC?

...sleep in a pool of vigilance so bright...

You may have moved past this but here's my 2 cents anyway.

The self-aware AI who see's something that is kind of like itselfish but not really...it's going to want EVERY SINGLE PIECE of information on that something (your MC) and it's going to not want to share it. It might not be trying to help her at this point but it might monitor every single input for signs of MC and yank those over into it's private highly encrypted corner before it goes anywhere else.

Does not read and follow label directions.

The AI that she spawned is helping her, at this point. I have a plan for where that's going, and it ain't pretty...

What she has to work on avoiding is the first AI, the one that basically controls the whole system. The world in which this is set is Earth, but far, far in the future. Highly advanced tech, there are bioscanners EVERYWHERE, not to mention advanced satellites.

I'm debating on some adjustments to my primary AI, whose name is currently Jacob. He is, of course, going to have to react to the presence of this new AI, which has been successfully hiding from him for years, but by helping my MC escape has pretty much made sure that Jacob is fully aware of it's/her presence. (In my mind, first AI is male, and second AI is female, simply because the people whose brain patterns sparked their initial awareness were respectively male and female...)

Hopefully this is making some sense...

Once she gets to the church, no problem... plot plays out from there...

But is that really the first place she's going to go? Because she's just had her entirely world utterly shredded. And now this unknown voice is telling her to go somewhere, would she trust it? Would she go there? Or would she do something else?

That's what I'm struggling with right now. She'll get to the church eventually, but will there be a side trip?

Oh, and second AI, which is helping her, turns out to be vastly more problematic for the world than Jacob... but that's for the sequel :D

NaNo 2009 - Simple Human - You are but a simple human whose mind cannot fathom the greatness that is The Collective.

If her AI (does she get a name?) is helping her not only could it be monitoring everything to basically get to it before Jacob (she'll know better what she's looking for than he will). This could also be a great opportunity for her to confront Jacob and keep so much of his circuits busy that your MC is fairly undetected.

Going to see if she can just get one last peek at her husband and kids and maybe grandkids (I can't remember if she has either but if she does yeah that). She might try to get a weapon.

I can't believe you are already 13K plus words in!

Edit for a possibility....is your MC super practical? If so she'd get a sturdy vehicle, make sure her family knew where everything they would need is, she would get food and drugs and storage for all these things (bags in the vehicle etc), she'd get something that resembled recording equipment. Then she would put her hands on a good weapon with LOTS of ammo and make sure she knew how to use it.

Does not read and follow label directions.

Second AI will get a name, I just don't know what it is right now! In my head, she wants to call herself Cassandra, which is, of course, Cassie's name. But that could be confusing and problematic for the reader.

She's 30ish, so no grandkids, and she has no children, either.

The husband? Well, let's just say the jackass was in on the whole Jacob thing... he knew all along and was specifically assigned to get close to Cassie... lovely sort of guy... part of the shit hittiing the fan for MC was discovering her husband was in on it. Ouchie!

She would be very practical, but now I've got her going a bit crazy at the moment... considering she just had unknown amounts of data downloaded to her brain by as-yet-unnamed second AI, she's kinda sorting through that...

Keep the ideas coming... may use them later on!

NaNo 2009 - Simple Human - You are but a simple human whose mind cannot fathom the greatness that is The Collective.

you need to read "The Hero's Journey" it will intimately educate you in the journey a character takes in any great tale.

~Jesse James Akins

I've been watching "The Wire". The crooks communicate with old-school pagers, since those can't be traced the way modern cell-phones can. Maybe take that concept to an extreme; your MC simply employs some archaic techniques that the big bad bloodhound machines aren't used to dealing with.