Not long after the events of the last episode, Darien will be dead, and the gland will be out of his head.
We have seen multiple times that, no matter how good his intentions, without the need for regular injections, he tends to wander off. The Official stated outright that if The Keeper cured him of the need for the injections, he'd have to kill him to put the gland in someone more reliable. Darien knew that and knew that he couldn't run away and hide.
Initially, he placed himself under the protection of the FBI and worked for them. In that situation, he was still doing what The Official wanted (as revealed at the end) and was protected by the number of people aware of him. But by the end of the series, he has quit the FBI and returned to The Agency. He hasn't signed the contract The Official offered him. He's insisted that he be allowed to work only when he wants and only on cases he thinks matter. And The Official, with whom he is so angry, has revealed some of the extent to which he has manipulated him. Even without the last few seconds with The Official at the end, it's clear this is unsustainable.
The Official will find some way to re-leash him.
Either by reversing the injection The Keeper gave him, or by finding some new thing to infect him with. Or, he could find something to control Hobbes or Claire and work through Darien's new-found loyalty to them.
The whole resistance-to-Counteragent thing was faked from the beginning.
When Claire gave Darien an injection at the end of the series, several viewers commented that it didn't look like Counteragent, it was too pale. Later, when Darien tells Arnaud, the guy who created Quicksilver Madness and the Counteragent in the first place, that he was developing a resistance to it, Arnaud's immediate response was, "That's impossible!"
So, what if the reason Darien wasn't responding to the Counteragent as well as he used to wasn't because he was becoming resistant, but because the Keeper was diluting it to convince him he was? Evil!Keeper option is that she was manipulating him to cement his loyalties, Good!Keeper version it would be the Official ordering her to, but Claire couldn't go through with his plans, and thus provided the cure.
Kevin Fawkes and Arnaud created Quicksilver Madness and the Counteragent together.
We know Kevin lied to Darien about just about everything. Darien wasn't the first person they put the gland into, and terrible things happened to the last one. Kevin was involved in other nasty human experiments before that with even worse results. And Kevin told Darien he could take the gland out as soon as they tested it ("It's only for a couple of weeks!"), when he was really at least a year away from figuring out how. Just when and how did Kevin plan on telling Darien, and how on earth could he keep his thief brother from running off to rob banks and make precious gems disappear?
When Arnaud first offered Darien the Counteragent in exchange for working for him, he said something odd. "You can't resist, believe me, I know. I helped design it that way." Given Arnaud's ego, even if he'd had underlings doing the bulk of the work on QSM and CA, he would have considered it his own creation. The only way he'd have said he'd *helped* design it is if someone else more prominent was in charge of that little side-project. Who knows more about the gland, or has more reason to keep Darien a part of the project whether he wants to be or not, than its creator?