It takes time, which Bruce was expecting, and it takes effort, which Bruce was expecting, and it takes a little assistance from Diana's lasso, which Bruce wasn't exactly ruling out, but they finally do it. They finally track down Jack Drake's notes on what he calls "Jokerization."
The notes are horrific. A part of Bruce almost wishes they'd never found the notes, they're that horrifying. But Bruce is still glad they found the notes, because in those horrific notes about information for how to become Jokerized is also information for how to reverse being Jokerized.
That's the good news.
The bad news is that the reversing is meant as temporary. It last twenty-four hours exactly, and then the subject is once again Jokerized, which appears to be the permanent and "natural" state for the subject after all the experimentation to Jokerize in the first place.
It makes sense in a twisted way. The Joker is evidently who Jack Drake considers himself to truly be, given some of the disturbing comments he made while under the lasso's power. So in some awful logic, it makes sense that the "Jack Drake" face and name would be considered the "mask" for Joker, not the other way around.
Unfortunately, that means "Timothy Drake" is also the "mask" for Joker Junior, which means that completing the reverse process on Junior won't last for long. To give Junior a normal life, they would have to complete that reversing over and over to reset Junior into Timothy Drake, and from the notes, the reversing process is far from pain-free. So that's not happening.
And so Bruce turns to his friends once again.
Martian Manhunter offers his expertise on shapeshifting, as do Hawkman and Hawkgirl. The Flash gives input on chemistry and about a hundred other areas of scientific research, one by one, as soon as he finishes speed-reading whatever he can find about each one. Wonder Woman continues to work with her lasso on Joker. Zatanna contributes magic, while multiple Green Lanterns contribute their version of science-that-looks-like-magic, and so on. Superman coordinates the efforts and reports to Batman, and Bruce thanks them all more effusively than he thinks he's ever thanked anyone before.
And eventually, they come up with what looks like a solution. Then comes the next step: getting Junior to agree.
Bruce isn't going to just make Junior do this. Junior has had enough choices taken from him in his short life. But Bruce is going to firmly emphasize how beneficial this process could be for Junior. Bruce has a whole PowerPoint prepared, plenty of sources to back him up on both the process and the probable benefits, several Justice League members at the ready for interviewing…
But when he brings it up, Junior just nods and says, "Okay. When do we start?"
Bruce blinks down at him.
From his spot snuggled up against Bruce's side, Junior blinks up at him in turn.
"What?" Bruce says.
Junior says again, "When do we start? Or do I have to-"
"Hold on," Bruce says. "I said we came up with a way to permanently unJokerize you."
"And I said okay," Junior says, sounding confused. "You want me to do it, right?"
"Right," Bruce says, starting to see where this is heading.
"So okay," Junior says.
Bruce sighs. "I don't want you to do it because I want you to do it. I want you to do it because you want you to do it."
Junior's face scrunches up. "What?"
Bruce thinks for a moment. "From what I understand, all your life, you've done what your father wanted you to do. Everything exactly as he said, and nothing to go against him. Is that understanding correct?"
"Yes," Junior says, then he looks away. "Almost yes."
"Almost?" Bruce asks.
"There was one thing I did against him," Junior says quietly, then he squirms a little.
Bruce hums quietly and wraps his arm more tightly around Junior, letting Junior think.
Eventually, Junior whispers, "I showed Harley the stuff about Ethiopia."
Bruce sits there. Absurdly, he wonders if this is what being struck by lightning feels, and if he can compare notes with Barry Allen. After a moment, Bruce repeats, "You showed Harley the stuff about Ethiopia. You gave away Joker's plan to her."
"And she saw me, just a little, and because she doesn't get kids involved, she broke back away from Joker, and she let you know about Ethiopia," Junior admits.
"And so I got there in time," Bruce says in a murmur, his mind whirling with what might've happened if he hadn't come home from patrol so soon, if he hadn't known where to look and what to look for, if he hadn't gotten to that warehouse in time. Bruce wraps his arm around Junior even more tightly. "Oh, sweetheart."
They sit there in silence for a while.
"That was the one thing I did against him," Junior says. "But I'm glad I did it."
"I'm so glad you did it too," Bruce says fervently. "And that brings me back to my point. I don't want you to live your life doing just what other people tell you to do. I want you to have your own life as an individual. And while I would prefer for you to be able to have that life as a normal kid, without the influence of Jokerization hanging over you, I don't want to force you to do that. I want it to be your choice."
They sit in silence again for a bit.
Junior breaks the silence once more, leaning back slightly. "I don't think I'm ready to get unJokerized yet."
"That's all right," Bruce says.
"But," Junior says, and then he hesitates. He starts again. "But the important thing there is the word 'yet.' I'm not ready yet, but I think I will be eventually."
"And I think that's a great choice," Bruce says.
Junior leans back into his side, and Bruce hugs Junior more tightly once again.