He was. He was captured at the end of Clear Sky thanks to the involvement of Scar (also an agent), except C-Con mistakenly took him as another member of the group (judging by the photo in Marked One's PDA in SoC, likely Ghost) and programmed him to kill Strelok. And over the course of SoC, as his new personality nicknamed "Marked One" he followed in his own footsteps taken as Strelok, rediscovered his past and regained some of his old memories via flashbacks.

But technically Strelok no longer exists since Clear Sky, it's just that Marked One kinda picked up where his old self left off and he's no longer working for the C-Con.

Originally posted by Mr. Fusion:

He was. He was captured at the end of Clear Sky thanks to the involvement of Scar (also an agent), except C-Con mistakenly took him as another member of the group (judging by the photo in Marked One's PDA in SoC, likely Ghost) and programmed him to kill Strelok. And over the course of SoC, as his new personality nicknamed "Marked One" he followed in his own footsteps taken as Strelok, rediscovered his past and regained some of his old memories via flashbacks.

But technically Strelok no longer exists since Clear Sky, it's just that Marked One kinda picked up where his old self left off and he's no longer working for the C-Con.

I'm aware of the original trilogy's story, I'm just trying to figure out if his autonomous or not

He works against the C-Con in HoC, and as far as we can tell, they are the only one with the ability to program agents. Since he lost his original C-Con programming during SoC, and became a new version of Strelok, this should mean now he does what he does on his own free will as he never could get a new program.

There is one hint that may suggest he was still somehow recaptured (but how? the Scorchers were offline, the Monolith was gone, the C-Con lost its connection to the physical world) and reprogrammed between SoC and CoP (and instructed to infiltrate SIRCAA or its predecessor to sabotage it), but it contradicts the part of the story which explicitly says that the C-Con lost their connection to the X Network after Strelok killed their bodies, and thus became unable to control anything, including their former agents, which either went to sleep or rogue after that.

But it is not clear where those "instructions" actually come from. It's a recording that he made for himself, but it's in a similar form in which the reframe messages other agents received were. I took it as a form of "auto-suggestion" if you will, him making sure that no matter what may happen to him, on subscious level he would still work torwards his goal driven by a "program" he gives to himself like an agent programming wouid.

He's as much against SIRCAA as against everyone else, so at times it may seem he's doing what would be in the interest of the C-Con. But in the end, he just wants SIRCAA gone and all the X Network taken down irreversibly so that the C-Con living in the noosphere also loses access to the Zone for good.

So, he may be an "agent" of himself, but I don't think/see how he could be an agent for anyone else as what he does ultimately serves no one else but him and the Zone.

Originally posted by Mr. Fusion:

There is one hint that may suggest he was still somehow recaptured (but how? the Scorchers were offline, the Monolith was gone, the C-Con lost its connection to the physical world) and reprogrammed between SoC and CoP (and instructed to infiltrate SIRCAA or its predecessor to sabotage it), but it contradicts the part of the story which explicitly says that the C-Con lost their connection to the X Network after Strelok killed their bodies, and thus became unable to control anything, including their former agents, which either went to sleep or rogue after that.

Maybe Faust "recaptured" him?

The real question is how Strelok affort the march armies he sends after you and all his gear he has, teleporting around like its nothing. He cant really be that independent.