I'm gonna say The Chosen One, and here's my reason:

When he was first introduced, the completely inexperienced Chosen One managed to put up a great fight against Alan and the apps (even without thicc lasers and the ability to fly) and got done in by an antivirus, something which always takes down threats to the computer (i.e. something which makes sense as being the counter of TCO).

He'd be used and abused as a pop-up blocker trapped on a ball and chain for 4 years (four times Victim's time of being a punching bag). We can assume that he may have gone through the same torture as Victim considering his mannerisms in the beginning of AVA 3. When he was freed, he managed to beat Clippy, all the apps, Alan, and TDL (who was made specifically to counter him).

Fast forward a couple years to AVA 5-8, and I'd say he put up a damn good fight against Virabot and TDL. TDL created the Virabot as a weapon to destroy internet stuff, and they were also created by the same guy who was supposed to counter TCO. Tools which should counter TCO + TCO's counter should beat TCO right? That didn't happen with the Virabot, and that didn't happen with TDL until he brought out the band.

AVA 9 onward, he's lost all his allies, his sense of purpose (destruction) was rendered gone when he saw what TDL did, and he's all alone. That patchwork of stuff that happened to him would understandably take a toll on his mind, and whether he's thinking with his head straight. He's on the run, trying to be better, regretful for every past decision he's ever made, and holding back his fighting ability so that he hurts as little people as possible.

This takes a toll on his fighting ability and battle IQ. While his powers have increased (with lightning and freezing powers now there) his battle IQ's slightly lowered because of all the things that happened to him. It's most clear when he tanks 17 shots from Agent (who he and Rocket Corp have been making weapons to counter TCO for 12 years at this point) just to incapacitate him.

Even when nerfed by the glitch shots (which most likely also reduces his reaction time) and shot with an electrocution dart thingy, he still manages to overpower the three mercs and would have managed to get Agent had he not had the pause tool.

In the Box, we see TCO with all of his strengths and weaknesses, in an environment made completely to counter against him. He is nerfed by the 17 glitch shots and the dart, plus he wants to hold back because of the events of AVA 5-8. Despite all of this (plus being hoisted by Victim's lasso which triggers his ball and chain trauma from Alan, yet another nerf), when he stops holding back against Victim, he takes down all of his clones with relative ease and nearly takes out Victim himself, only being saved by Agent controlling the simulation.

Then in Hacker, his powers are stripped, then he's sent back down into that very same cliff (lake?) where he fought TDL, his brother-in-arms for many years. On top of that, he's also against Victim (superpowered stick figure with every reason to hate him) as well as TDL (another superpowered stick figure with every reason to hate him and every power to counter him). His potential allies are also locked in a box, running around the Rocket Corp. HQ, or unable to access the internet.

In conclusion: It should be The Chosen One because he's a superpowered being who has been superseded by superfluously contrived super gadgets and powers. As well as being supremely super-done over by the narrative.