This takes place during the balcony scene in 2x05 when Alec and Magnus are having a heart to heart. Consider it an extended scene.
"I still can't face her, Magnus....I can't go back to that institute."
Magnus looked down at Alec's hands. They were bruised and covered in cuts from overusing his bow. He'd refused to use a healing rune in hopes that the pain in his hands would overpower the pain in his heart. Magnus knew exactly how he felt. He once thought physical pain would cover up the emotional one too. "You will. You have to. That's who you are, Alec. If you don't face her, that guilt you're feeling will eat you alive and destroy you-"
"I killed her mother, Magnus!" Alec shouted. His voice broke and he swallowed in attempt to steady himself. "I killed Jocelyn. Her blood was on my hands. She died by my hand. Clary's mother....Jace's mother."
"Alec....it wasn't your fault. It was the demon's." Magnus leaned against the balcony ledge where Alec had kept his distance the entire time. "Don't beat yourself up over this. Please. It kills me to see you this way. The physical pain I can help you with but it's the emotional stuff that's a little harder to heal with magic."
Alec leaned back and pressed the palm of his hands against his eyes. "I feel so broken. I doubt even magic can piece me back together."
"And most often magic can't. It's up to you whether or not you want to put back together again." Magnus cocked his head slightly. "You know the story of Humpty Dumpty, right?"
Alec scoffed. "Let me guess. You knew him back in the day too?"
Magnus smirked. "No. But the moral of the story is very similar to your predicament. When Humpty fell off the wall, he shattered. He became broken. Not even all the king's horses or all the king's men-"
"Couldn't put Humpty together again. I know the story. But what does that have to do with me?"
"Patience. I'm getting around to it," Magnus snapped his fingers and the lights above their heads lit up. "There's another few lines to the nursery rhyme that got lost over time. I can't really remember how they go but I do remember this. Humpty pieced himself back together again. Bit by bit. It took a while but eventually he became whole again. Just like I know you will be whole again too."
Alec watched Magnus with teared filled eyes. "Did he ever get back up on the wall again?"
Magnus shrugged. "I'm afraid that part's been lost over time too. I can't remember. It's been so long since I actually quoted any children's rhymes," he chuckled to himself. "But you get my point though. Sometimes only you can put yourself back together again. I can help you, but there's only so much I can do. My powers are limited."
Alec turned to look down at the busy streets of Brooklyn below them. He thought back to when he was scaling the wall to reach Magnus' balcony and how much his hands screamed in protest. But the pain felt so good. It made him forget about the ache in his heart. The guilt. The remorse. It was just enough to make him feel good for a moment but not quite good enough to be permanent.
"You're probably thinking I'm crazy, quoting Mother Goose to you. I'd understand if you did," Magnus too turned around and looked out at the city. It looked beautiful at night.
"No. I don't. If I did, I wouldn't have ran here to get away from everyone," Alec said in a quiet voice. He looked over at Magnus. "You were the first person I thought of. I feel..." He sighed through his nose. "I feel safe here. Like I can come here and just let everything out."
Magnus nodded. "I'm glad you feel that way. My home is always open to you, Alec. If you ever need to just get away and let out some steam, don't be afraid to knock on my door. Or scale my balcony," he smirked as Alec laughed softly. "My home is your home. Never forget that. I won't ever judge you for wanting some solitude. God knows that's all we need sometimes."
Alec looked down at his injured hand and sighed. "I should be getting back. Jace is probably looking for me."
Magnus nodded. "Yeah. Okay. But you'll think about what I said though?"
Alec gave him a solemn look. "I have to go."
Saying nothing more, Magnus stepped back into his loft. It was only when Alec was about to jump down off the balcony did he speak up again.
"Alec?" He said.
The Shadowhunter paused. Half of his body was already hanging over the edge of the balcony, his forearm muscles flexing as he held on for balance. "Yeah?"
Magnus frowned. "I have a front door, you know. You can use that instead."
Alec bowed his head and chuckled. "I'm fine. I need the exercise anyway."
And with that, he let go. Magnus almost yelled in protest but when he leaned over the ledge, he saw that Alec had landed safely on the ground below in a crouch and was slipping on his jacket as he walked.
"Crazy Shadowhunter," Magnus mumbled to himself before he went back into his home and kept the the patio doors behind him open.