The MC has a system where the ML can hear and respond to. So basically, the ML knew he is the target and because of that he interacts with the MC subtly.

The ML is both the System AND the Target and the Fact the Target ML CAN SEE the System Panel and Interact to MC LIKE A SYSTEM. Thought what he can see was Limited.

The 1st chapter would explain it, but if you get confused I will explain the simple way:

System = an Intellectual Computer that happen to be binded to the Main Body of ML. Simple explanation is; it's like a Genius Computer (probably AI but not the sentient type) that should have given to MC, but accidentally given to ML, but still linked to MC.
Target = Fragments of ML, so they all can see the Panel System and use it within limit and can talk to MC. BUT the one who give Missions, Information and all is THE MAIN BODY. And of course they don't know they all just a soul fragments from a Someone.

ML is sealed away by a godly force/organization that an amnesiac MC is now working for.
It's indicated from the beginning that they're lovers through the hints the author gave away as inexplicable longing and closeness they felt towards each other.

While ML shows a crazed obsession for possession and control, the MC tolerates this psycho-lover with unlimited patience and undisguised criticism. Both are equally aware of much of a bad person the ML is yet MC believes he can be calmed down through the love he gives him, yet is determined to put him back under control and shackles of their organization for the greater good.

Will ML be locked up by MC for good this time or will they find a way to freedom and live happily ever after?

It's a Chinese web novel, so the ending is quite on the nose.

So, the main problem for me in this story was the lack of romantic emotions. ML is crudely forward in his demeanor and shows it through possessiveness and obsession and MC is the only key to calm him down.
Though MC enjoys his company, he's indignant somehow over his true feelings and refuses to be honest leading to many many misunderstandings while knowing the ML is desperate for affirmation and security, MC loved to play with his feelings.
Even if he'd think of other people more suitable than ML, every time he got closer to another person other than the ML, he'd feel repulsed.
They both treated each other insincerely yet are inseparable from each other. But nevertheless, he was forced to coax the ML through ML hijacking the main system to begin with and would be punished physically with pain and drained strength if he wouldn't comply.

The ending was ridiculous. For nearly destroying the planet and killing many lives, ML's prison time was treated like a time-out.
On the promise of good behavior, he's let out. The whitewashing (his innocence) was laughable, vigilante self-served justice in the name of revenge and undermined crimes, painting the guy as a troubled teen.
As mentioned before, only ML is deserving of salvation, the rest who had experienced and lived the same as him will be cannon fodder to spice up the story.

The 2nd arc ML was the sole endearing one as he's not committed or plans to commit crimes beyond redemption unlike the rest and has an immaturity that creates a sweet and clumsy gap-moe from his usual cold nihilistic deranged self.