Padmé was called to an emergency session of the Senate while Obi-Wan and Yoda broke into the Temple to send a message warning the remaining Jedi not to return to the Temple. While they're there, Obi-Wan checked the security tapes and watched Anakin cut down younglings and one of the troopers refer to him as "Darth Vader."
Yoda sent Obi-Wan to dispose of Darth Vader. Only after telling Obi-Wan that Anakin no longer existed does he agree to find him.
"Use your feelings, Obi-Wan, and find him you will."
Searching his feelings, Obi-Wan discovered he couldn't think about finding Anakin until after he'd found out if Padmé had escaped his wrath.
At the Senate, the Chancellor told everyone his story of the Jedi trying to wrest control of the Republic. His hold on the majority of the remaining Senators showed as they applaud his announcement that his title will change from Supreme Chancellor to Emperor.
Shaken, Padmé went home to find Obi-Wan waiting for her. She told him about the Emperor, and he told her about Anakin's change.
"No. Not Anakin. He would never do something so despicable!"
"I saw it with my own eyes."
"Everyone saw everything with their own eyes, today. Is there anyway that one of you could be wrong?"
"We can both be right. Master Windu was a student of Vaapad. It is possible he decided that Palpatine would be safer dead rather than captured. But Anakin is capable of very nasty things. I- I wonder if you would permit me to try something on you."
"Will it hurt the babies?"
"No. I promise."
"Okay."
Obi-Wan reached out and placed his fingers on Padmé's forehead. He could feel her mind, a jumble of orders and contradicting orders, held together by jealousy, greed, and hate. Using the Force, he removed all of the suggestions Anakin had placed on her.
Padmé gasped as her mind was freed, and burst into tears. Obi-Wan held her until she'd composed herself.
"How could he do that?" she asked. With the restraints gone, she was able to reason the connection between his orders and her immediate obedience. No longer blinded by love, she knew he was capable of turning to ambition and power and killing innocents.
"His ambition exceeded his love. He decided he'd rather have you than wait for you to love him."
"I missed you so much. Deep down, somehow I still loved you. It always made him angry, whenever I mentioned you. I dreamt of you. I didn't know it, I couldn't see your face, but I could never reach you."
"I'm here now," he said, holding her.
He felt one of the babies kick against him. Obi-Wan pulled back to look at her belly.
"Anakin is the father, isn't he?"
Tears falling, Padmé nodded. "You and I always used protection. Anakin never did. It might have been possible, if we hadn't been so careful. But I'm sure they are Anakin's. I wish they were yours," she whispered.
"Do you know where Anakin is?"
Padmé nodded. "Are you going to kill him?"
"I might have to. With the Chancellor taking power as an Emperor, and the Jedi betrayed, if I can't convince Anakin he's on the wrong side, for the sake of the galaxies, I might have to kill my Padawan."
Padmé shook her head. "I hate him for what he did to me, but I can't tell you where my children's father is if you're going to kill him. You'll have to find him on your own."
Obi-Wan nodded and stood to leave. "I'm so sorry. For all of you."