This scene was in the ARC for Ashes but was later deleted. It's a good scene for Isabelle, I think, but wasn't really necessary to the story. It begins at exactly the top of page 288 in the hardback US edition of City of Ashes.
"How convenient. Everyone's either unconscious or apparently delirious," said the Inquisitor. Her knife-like voice cut through the room, silencing everyone. "Downworlder, you know perfectly well that Jonathan Morgenstern should not be in your house. He should have been locked up in the warlock's care."
"I have a name, you know," Magnus said. "Not," he added, seeming to have thought twice about interrupting the Inquisitor, "that that matters, really. In fact, forget all about it."
"I know your name, Magnus Bane," said the Inquisitor. "And quite a bit more about you, besides. You were raised by the Silent Brothers of Madrid in the seventeenth century. They named you and turned you out on the world when you were sixteen. I know the things you've done, things you'd rather stayed hidden. It took you this long to build up your reputation; a word from me could tear it down again. So consider very, very carefully, if you wish to remain involved in this situation. You've failed in your duty once; you won't get another chance."
"Failed in my duty?" Magnus frowned. "Just by bringing the boy here? There was nothing in the contract I signed that said I couldn't bring him with me at my own discretion."
"That wasn't your failure," the Inquisitor said. "Letting him see his father last night, now that was your failure."
There was a stunned silence. Alec scrambled up off the floor, his eyes seeking out Jace's -- but Jace wouldn't look at him. His face was a mask.
Luke spoke first. "That's ridiculous," he said. Clary had rarely seen him look so angry. "Jace doesn't even know where Valentine is. Stop hounding him."
"Hounding is what I do, Downworlder," said the Inquisitor. "It's my job." She turned to Jace. "Tell the truth, now, boy," she said, "and it will all be much easier."
Jace raised his chin. "I don't have to tell you anything."
"Really?" The Inquisitor's words were like the flick of a whip. "If you're innocent, why not exonerate yourself? Tell us where you really were last night. Tell us about Valentine's little pleasure boat."
Clary stared at him. She could read nothing in his face. I went for a walk, he'd said. But that didn't mean anything. Maybe he really had gone for a walk. But her heart, her stomach, felt sick. You know what the worst thing I can imagine is? Simon had said. Not trusting the person you love more than anything else in the world.
When Jace didn't speak, Robert Lightwood said, in his deep bass voice: "Imogen? You're saying Valentine is -- was -- on a boat?"
"In the middle of the East River," said the Inquisitor. "That's correct."
"That's why I couldn't find him," Magnus said, half to himself. He still looked stunned. "All that water -- it disrupted my spell."
"But how would Jace even have gotten there?" Luke said, bewildered.
"Shadowhunters are good swimmers, but the river water is freezing -- and filthy --"
"He flew," said the Inquisitor. "He borrowed a motorcycle from the head of the city's vampire clan and he flew it to the boat. Isn't that right, Jonathan?"
Jace had dropped his hands to his sides; they were clenched into fists. "My name is Jace."
"There is no Jace. Jace is a ghost, a construct you and your father invented to fool the Lightwoods into loving you. You're your father's son and you always have been."
The Inquisitor turned to Isabelle. "Go around the side of this house," she said. "You'll find a narrow garbage alley. There's something blocking the far end, something covered with a tarp. Come back and tell us what it is."
"Izzy." Jace's thinned with strain. "You don't have to do what she tells you to."
Isabelle's dark eyes were snapping like firecrackers. "I want to. I want to prove to her that she's wrong about you." She spoke as if the Inquisitor wasn't there as she rose to her feet. "I'll be right back."
But she was gone, the door falling softly shut behind her. Luke went over to Jace and tried to put a hand on his shoulder, but Jace shook him off and went to stand by the wall. The Inquisitor was looking at him greedily, as if she meant to drink every drop of his misery like wine. Vicious bitch, Clary thought. Why is she torturing him like this?
Because she's right. The answer came as if another voice, a treacherous voice, were speaking inside her head without her desire or permission. He did exactly what she said he did, look at his face.
But Jace's face was a blank, his eyes all that lived behind the smooth, unruffled façade. Maybe this was all part of some plan of his to discredit the Inquisitor. Though she didn't look as if she feared discrediting, she looked --
The front door flew open with a bang and Isabelle marched back into the room, her black hair whipping around her face. She looked from the Inquisitor's expectant face to her parents' worried ones, from Jace's set jaw to Alec's furious scowl, and said, "I don't know what she's talking about. I didn't find anything."
The Inquisitor's head whipped back like a king cobra's. "You liar!"
"Be careful what you call my daughter, Imogen," said Maryse. Her voice was calm but her eyes were blue fire.
The Inquisitor ignored her. "Isabelle," she said, lightening her tone with an obvious effort, "your loyalty to your friend is understandable --"
"He's not my friend." Isabelle looked over at Jace, who was staring at her in a sort of daze. "He's my brother."
"No," said the Inquisitor, in a tone that was almost pitying, "he's not." She sighed. "You do realize what a serious breach of the Law denying information to an officer of the Clave is?"
Isabelle lifted her chin, her eyes blazing. In that moment she looked like nothing more than a smaller copy of her mother. "Of course I realize it. I'm not stupid."
"Christ, Imogen," Luke snapped, "do you honestly have nothing better to do that bully a bunch of children? Isabelle told you she didn't see anything; now leave it."
"Children?" The Inquisitor turned her icicle gaze on Luke. "Just as you were children when the Circle plotted the destruction of the Clave? Just as my son was a child when he --" She caught herself with a sort of gasp, as if gaining control of herself by main force.
"So this is about Stephen after all," said Luke, with a sort of pity in his voice. "Imogen--"
The Inquisitor's face contorted. "This is not about Stephen! This is about the Law!" She turned on Isabelle, who shrank back, startled at the fury on the older woman's face. "By defying me, you break the Law, Isabelle Lightwood! I could have you stripped of your Marks for this!"
Isabelle had recovered her composure. "You can take your Law," she said in a measured tone, "and shove it right up your--""She's lying." The words were spoken flatly, almost without affect. It Clary a moment just to realize that it was Jace speaking; he moved to stand in front of the Inquisitor, partly blocking Isabelle from her view. "You're right. I did everything you said I did. I took the cycle, I went to the river, I saw my father, and I came back and stashed the bike in the alley. I admit to all of it. Now leave Isabelle alone."