Spock (alternate reality)/Relationships/Friendships/Leonard McCoy

Although McCoy originally admired Spock from afar after seeing him best Kirk during a regarding the cadet's cheating on the , their relationship quickly became complicated. ()
In 2263, after working aboard the same ship for some years, Leonard McCoy and Spock weren't exactly best friends yet. When the ship got to Starbase Yorktown for a break, McCoy accidentally witnessed a sad moment between Spock and as the man sadly looked after the woman walking away from him. Knowing about their romantic relationship, he ironically asked Spock if they were breaking up and promptly assumed it surely was because of something the Vulcan had done.
During the dramatic moments aboard the Enterprise following Krall's swarm ships attack, Spock and McCoy teamed up and got to the damaged ship sectors so that McCoy could check on the injured crew. During this time, they both got trapped into a turbolift that was subsequently expelled from the ship into space, and intercepted by one of the swarm ships. Not without effort, the two men successfully defeated the swarm drones aboard the vessel with McCoy taking control of the ship, and both of them looking in disblelief and fear as the enemy ships captured crew members that were leaving the hopeless ship in escape pods. 
As a consequence of their harsh landing on the planet Altamid's surface, Spock got severely injured on his lower abdomen and McCoy pointed out that with the Vulcan heart being placed where the human liver is, he was lucky the injury was located an inch away from it or he would have been killed instantly. With no medical equipment available to him, the doctor was forced to cauterize and seal Spock's injury the best he could using the heat produced by a phaser. 
Later, when the two of them reached a cave to rest for a while, McCoy got concerned about Spock when the latter looked unconscious, and he tried to wake him up. Spock replied that he had closed his eyes to simply contemplate mortality. After a moment, in visible distress both physical and psychological, Spock confided to the doctor that the reason for the tension he had witnessed between him and Lieutenant Uhura before was the fact that he had started to be unsure about his place in Starfleet and wondering about whether he still owed a debt of duty to his endangered species, and the recent news about the death of Ambassador Spock had further persuaded him that he needed to leave Starfleet to help his people on New Vulcan. McCoy wondered about what Captain Kirk would have thought about it, to which Spock answered he had not told him about his decision yet. McCoy joked that if Spock left, he'd throw a party and, to his surprise Spock smiles, a detail that made him realize that the man was indeed delirious because of his injury.
Having understood that they needed to get out of their refuge to attempt to contact the surviving crew, the two men left the cave, which exposed them to the drones. Spock asked the doctor to leave him behind because it was important for him to find the rest of the crew, but McCoy refused to leave him there and sarcastically commented that for a moment he thought Spock cared about his well being too, to which Spock replied, as the swarm ship were getting close to them, that he thought his respect for him had always been clear in spite of their not always friendly dialog through the years. 
After getting beamed to safety aboard the USS Franklin on time, McCoy finally tried to medicate Spock's injury using some of the old, albeit less effective, medical equipment they found on the ship. Later on, after Spock realized that they could track the Vokaya mineral of the necklace he had given to Uhura and find her and the rest of the crew still held captive by Krall, McCoy teased the vulcan about the fact that he had not only gifted radioactive jewelry to his girlfriend, but it also was a tracking device, much to Spock's chagrin and disbelief because that had not been his intention.
McCoy was understanding and supportive of Spock's decision to join the rescue team because of Uhura's presence in the base among the ones in danger, in spite of the Vulcan's physical condition still being impacted by his injury thus requiring him to stay behind and rest. After successfully saving the rest of the crew and finally leaving the planet aboard the Franklin, Spock volunteered to pilot one of the swarm ships in order to find the signal that made them move in sync and give the rest of the crew the required information to disrupt it and defeat the swarm before they could destroy Yorktown. When both Uhura and Kirk expressed concerns over his condition, Spock proposed that he could be helped by doctor McCoy because he, too, was more familiar with those ships after their shared experience on one of them. This, much to the Doctor's horror and annoyance over the prospect of piloting one of those vessels again. Despite his protests, the two men are able to accomplish their mission and ultimately save Captain Kirk in time before he's sucked into space after defeating Krall.
The experience on Altamid no doubt gave to both Spock and McCoy a new mutual understanding and respect of each other. However, the doctor still maintained some of his old mocking habits when he saw Spock chatting with Uhura at the party he had organized for Kirk's birthday, and he eyed her necklace in a manner that suggested he was still judging the Vulcan for giving to his girlfriend a 'tracking device'. 
Ultimately, Uhura and McCoy were the only people who knew about Spock's personal conflict.