AJ is alive and "well" - A Theory
Clementine has lied to us throughout the game, or at the very least she hasn't been too open about the truth and I think I know exactly what is going on when it comes to AJ. Now take into account, A New Frontier (ANF), isn't necessarily evil. They just seem to be a group of survivors who are more ruthless, from what we understand, we never hear or see them being like other groups that demand supplies or anything like that (though either they reused a model or it seems as if ANF took over Wellington in one of the endings, which is possible). However, one interesting note is that AJ isn't dead. Notice how his whereabouts are simply unknown, we never see or hear of him ever being hurt or being dead, so let's assume he's alive and was separated from Clementine.
I believe Clementine was in ANF where she later on fled with AJ to Richmond, leaving AJ there as she realised she was being hunted down or was simply a target and couldn't constantly look after "goofball". I mean in the 'Alone' ending and the 'Ava' flashback, we clearly see she has some difficulties with AJ, and reasonably she would. Despite the fact that Clementine is pretty competent, she is only a 13 year old girl with a 2 year old baby, with little to no experience of ever looking after someone so young beforehand. She has no support and she's alone.
So she joins ANF, who help look after AJ. However, after she realises something is wrong with the group, whether they grow more ruthless or she's forced to do bad things, she flees and is in Richmond where she gives AJ to be looked after (allowing her to visit), as she goes into the wild, scavenging for food and doing something else - trying to get rid of ANF.
Clementine notes that she was trying to stop the truck in order to drive it, she wants Javier's van in order to drive that somewhere, and she is adamant towards the man that she needs a box of bullets that can fire. All of these sound reasonable if she's just an everyday survivor. She needs a vehicle to move around, bullets for ammunition. But I don't think that's it. Coupled with the fact that Richmond seems to be a good few hours away due to having to drive there, and also the fact that whenever ANF, Clementine is the one who suggests they start shooting or telling Javier that they shot one of his family and they'll do it again unless they're stopped. Clem is almost ruthless when it comes to stopping these guys, so, what gives?
Well I think Clementine needed the vehicle, a box of bullets, and was planning on driving to Richmond to pick up AJ and then going to drive away somewhere else in the country. But she's taken the box of bullets not to just defend herself from people and AJ, but finish the New Frontier if she ever runs into them on the way.
When she panics that Richmond has been taken over, she is clearly worried for AJ and notes how they cannot see her at all, even wanting to "leave" the group as she said she'd "find her own way." Finding her own way, most likely means she is going to sneak in when the group is distracted, take AJ, and find her own way out. The New Frontier is expanding and her plans are less likely to try and murder them to at least put a dent, but simply is to escape. This also makes sense as to how she "heard" about Richmond in the first place.
Let's hope that Clementine gets to AJ in time, well that is unless you betrayed her.
Comments
Good points here. Yeah, it was definitely interesting that in our first interactions with Clem she is so focussed on getting a vehicle. Her mini-panic-attack after Jesus reveals that Richmond has been taken over can also support your theory that she has unknowingly left AJ in what is now NF territory. But the question is why she is so far from Richmond in the first place? From the dialogue, it seems like Clem has been dotted around Prescott for quite some time. There must be a reason why she decided to completely abandon AJ in the custody of others.
Maybe she thought she couldn't care for him anymore but wanted him to be well looked after with food etc or maybe she felt like she was putting her own life at risk by caring for AJ due to his crying attracting the Muertos/Walkers.
I imagine the reason is, she was worried that ANF were going to be tracking her down and since she's been with the group, she simply wanted to get AJ as far away from their territory as possible. She probably believed Richmond was safe enough and went back to deal with ANF on her own, all whilst staying at Prescott on occasion and getting supplies to help her in her endeavour, even trying to find a car so she could keep driving back and maybe just drive and leave Virginia altogether.