Any suggestions on how to strengthen this external conflict?

[Mammon]

You said that the MC's opinion of the system etc. was going to be a big issue, and I don't see why that couldn't in many ways act as the motivation or driving force for the story. As you said there could be a whole lot of opinions regarding the system but the safety and structure (everyone being fed while other cities are much poorer) is what's keeping the people obeying it. Look at the real world, there are hundreds of different ways this could be used and it's just a matter of picking one.

Not enough action in your story? There's a government unit that's looking into the project and might 'intervene' if they do find something incriminating so MC needs to make sure they don't get access to his laptop or something. Not enough tension? There are people who believe almost religiously in the system who might report MC to the government and tip off that government unit or act as judge and jury themselves. Or the antagonist might make these people believe things to urge them to do that. Not enough Philisophy in your story? Make the not-black-and-white system more present and the question of whether it's good or not more important. Want to make the system less uthopic? Harsh anti-immigration policies or non-citizens&people who failed to get as high-up as desired rebelling against the system could do that.
I'm shooting blindly here because I don't know what would and wouldn't work in your story, but there are plenty of real-life politics and similar stories that could serve as inspiration to your story.

I too see some resemblances with Psycho pass. The rest of the world being rather bad and the citizens in Japan being the only ones who can grow up peacefully (at least, according to the Japanese government...) while a supposedly unfallible system makes sure that everyone fits into society but with flaws in this system that no one wants to be revealed, it's a good start but never let yourself be led by one story saying 'this is how we did it, so this is how it has to be.' If something doesn't work, try to take some distance and see if there's something in your world-building that can be changed, expanded upon etc.

[Yunou]

You said that the MC's opinion of the system etc. was going to be a big issue, and I don't see why that couldn't in many ways act as the motivation or driving force for the story. As you said there could be a whole lot of opinions regarding the system but the safety and structure (everyone being fed while other cities are much poorer) is what's keeping the people obeying it. Look at the real world, there are hundreds of different ways this could be used and it's just a matter of picking one.

Not enough action in your story? There's a government unit that's looking into the project and might 'intervene' if they do find something incriminating so MC needs to make sure they don't get access to his laptop or something. Not enough tension? There are people who believe almost religiously in the system who might report MC to the government and tip off that government unit or act as judge and jury themselves. Or the antagonist might make these people believe things to urge them to do that.

Thanks! With this story, there always some kind of conflict going on scene-by-scene, but it's having an overarching conflict that brings the story together and serves as a logline that is giving me trouble.

The thing is that there is a ton of action going on in the story itself--a lot of what you pretty much covered. Their advisor tells them to stop, they don't listen, and it eventually causes serious consequences for them when they are discovered. There are definitely people who believe in it religiously even though they understand the flaws, there are those who are indifferent, and there are those who hate it--and there is definitely drive for certain characters to want to prevent MC from delving deeper for completely different reasons.

Not enough Philisophy in your story? Make the not-black-and-white system more present and the question of whether it's good or not more important.

I think that's pretty much the core of the story is that it is pretty philosophical, not preachy or anything at all, but it's all about MC struggling with the black-and-white views he's presented with and trying to decide for himself whether he personally believes in it. MC never really questioned how things were nor did he want to--he was raised in the upper elite class.

If I had to describe MC in two words it would be "unapologetically curious". This has never been an issue for him until he realises that the government doesn't really appreciate those sorts of efforts. He never realised how much of a role censorship plays in their lives and how much trouble one can get themselves into trying to get around it.

But at the same time, there is the issue of citizens vs. non-citizens. At first, it seems like a fine system, but then MC realises that it can be seriously abused. But then there are certain non-citizen characters who point out that they trade certain privileges for more freedoms--they aren't expected to work as hard at their jobs and they can choose their own romantic partner because marriage doesn't exist for them.

Want to make the system less uthopic? Harsh anti-immigration policies or non-citizens&people who failed to get as high-up as desired rebelling against the system could do that.
I'm shooting blindly here because I don't know what would and wouldn't work in your story, but there are plenty of real-life politics and similar stories that could serve as inspiration to your story.

Exactly. These exact issues are dealt pretty much dealt with--there are really harsh anti-immigration policies that are discussed because MC's boyfriend wants to leave the city, but if he does, he's not going to be able to return. There is also a rebellion discussed that happened ~10 years prior, but it's heavily censored (and also a pretty big part of the plot).

I kind of deal with MC interacting with people who failed to get as high-up as they had wanted, though it's not really as "high up" as unfavorable results. Such as not being placed in the track they had wanted or them dealing with domestic violence because they can't accept the conditions they are given. I think it would be interesting to shape a close character to MC as being utterly destroyed by working so hard for what they wanted and then being told they are fit for it.

I too see some resemblances with Psycho pass. The rest of the world being rather bad and the citizens in Japan being the only ones who can grow up peacefully (at least, according to the Japanese government...) while a supposedly unfallible system makes sure that everyone fits into society but with flaws in this system that no one wants to be revealed, it's a good start but never let yourself be led by one story saying 'this is how we did it, so this is how it has to be.' If something doesn't work, try to take some distance and see if there's something in your world-building that can be changed, expanded upon etc.

Oh yeah, I have never seen Psycho Pass (and I kind of have been avoiding it for this reason) so I am going off the whole "False Utopia" trope as a premise. I feel like overall, my scenes themselves are really strong and serve a necessary purpose and there is conflict within each scene whether it's just MC needing to desperately escape an uncomfortable situation or him trying to steal information from someone, but obviously these key points are flexible to being modified.

Like, I know that MC finds out something at a specific time because it leads to another big plot point, but the manner in which he finds it out or who is is with, or even, to an extent, what he finds out, can be easily altered to make more sense for the story.

Like your suggestion with a person not getting a high-up enough position--I have a character now who is pissed because he wasn't put on the track he wants, but I could bump him down in status and change that anger to devastation and rage.

Anyway, thanks so much for your help. I really appreciate it.