Authors Note: A few things before I start - this is set in an amalgamation of the Arkham-verse also with the CW shows and DC media in general.
As Batman swung through the streets of Gotham, he heard a familiar voice come through his radio...
"Joker has holed up in the old GCPD building - one of Batman's people went in there. They haven't come out, I want all units to set up around all exits. Non-lethal if possible, lethal if necessary."
Hearing that, Batman swung off towards the old GCPD Building...
"Are you sure this is a good idea?" Maggie whispered down the phone. "Joker is serious business."
"Yes, I'm sure. Batman won't mind. He might actually be impressed for once if I capture the Joker."
"Sorry, your too late - one of the Bats are here."
"Okay, I'm on call if you need me..."
"Okay, I'll be careful..." Maggie looks into the window that Batgirl entered, unaware of the trap inside...
"Gordon, what is the situation." Batman lands next to the Commissioner and Gordon turns.
"One of yours entered there 30 minutes ago and hasn't left."
"They didn't speak to me about this..." He turns away and nods slowly as someone talks to him through an earpiece. "Neither have they reported in. I'm going in."
"Batman." Batman turned and Gordon sighed. "Barbara hasn't answered my calls. She was around here yesterday, can you keep an eye out for her. Joker has also been shipping in various chemicals his gang stole. Our undercover cops called it in whilst escaping... they barely made it back." Batman nods and turns, grappling into a vantage point before swooping down and systematically taking out the snipers around the building, after the final one, he radios Gordon.
"Gordon, we're these snipers out here before?"
"No, why?"
"Joker has Batgirl and possibly Barbara hostage." Batman said those words with unwavering certainty - knowing that they were the same person.
"Be careful, Batman, my teams are on stan-"
"Gordon? Damn, communications jamme-" He is silenced by the gargoyle he is perched on exploding, raining fragments of rock and Batman onto the ground...
"hehehohohahaha... Whatever one of those Bats comes through that window, they are in for my funniest joke ever."
smash!
"Give it up Joker!" Batgirl swoops down and lands on top of what appears as an inconspicuous stack of boxes. "We know you've been smuggling in chemicals to use for some purpose, why?"
"For this." He presses a button and the box she's stood on opens inward, dropping her inside, upon falling into the box, she is hit by some of Scarecrow's fear toxin alongside Harley slipping inside the box and fitting her with Mad Hatter's Bat-cowl-shaped mind control device - then the chamber begins to be pumped with gas whilst she is in the dazed state slowly, her skin pigmentation turns paler and paler, her hair changing from the normal ginger to a green, her iris' following suit. Eventually, the gas cleared... and Batgirl looked like the Joker - big grin, redder lips, green hair and iris', very pale skin and demented cackle.
"She's ready, Mr. J!" Harley Quinn walks over and lets Batgirl out, pulling the Mad Hatter Device off and grinning. "She's perfect."
"Good! Me and the caped jokester will be going now, stay behind and look out for anyone - stop them from getting to us!" Joker grabs Batgirl and pulls her towards a truck, pushing the laughing lady into the back before hoping in himself and smacking the truck wall, the truck moving off.
Batman shook his head slightly as he came to, laying in a room with the skylight shattered, he is surrounded with glass, rubble and ash. He stood up and groaned softly as a thug sprints towards him, he uses his Batclaw to pull him off balance, he clothes-lines him and then slams him into the ground before crouching and knocking him out before rising and grappling into the window.
He enters through the adjacent window, his eyes scanning over the glass container and then the slim figure of Harley Quinn.