Mycroft had left Sherlock's bedside, but he was still resolved to protect his brother from the dangers of the world. He captured John Watson and interrogated him to see what kind of man he was. When he was satisfied that he was not a threat, he let him go.
Sherlock was a reckless creature still. He didn't understand the dangers of the world that he lived in. London was a lake brimming with dangerous creatures. Mycroft swam in this lake and fought the monsters there. His position in the British government gave him the power of a giant, but he was preoccupied with his own battles. It was hard for him to keep an eye on Sherlock and make sure that he stayed out of trouble.
When he heard that someone had abducted Sherlock and tried to kill him. He rushed to the scene only to find the villain was already dead. He saw his brother amongst the flashing lights, and he knew from a glance that John Watson had killed the man. Watson had protected Sherlock when Mycroft had not been there. Sherlock liked Watson. He smiled at him as warmly as he had once smiled at his dog, Redbeard. And Mycroft wondered. "Could this fellow protect Sherlock in Redbeard's place? Can I trust this man to guard Sherlock's back."