Kirk is the new villain.
Khan's blood over the course of a year has altered his thinking and behavior and has compromised his command of the Enterprise. The Klingon war has begun and Kirk feeling on top of the world and feeling confident successfully defended various Federation territories, his newly found aggression and intolerance was all too obvious to Spock now and during another brief (albeit avoidable) engagement with the Klingons, Kirk commands the Enterprise to destroy a mysteriously crippled battle cruiser instead of sparing it.
It would have been a chance to demonstrate a token of peace to end the war...
Kirk rationalises his decision that showing mercy to the Klingons who yearn to die to a superior opponent in battle would be most illogical.
Starfleet orders Spock to relieve Kirk and return the Enterprise. Spock and McCoy realises their fears and suspicions about Kirk, and agreed to improvise. They navigate the Enterprise into deep space to buy some time.
Dr Marcus and Spock work on a prototype transporter therapy (McCoy objects to this) to filter out Khan's blood cells in an ambitious attempt to save Kirk. Spock reasons with Kirk and convinces him that he must allow him to help him, he argues that he has never felt so good and confident of himself but says he trusts Spock. He reluctantly agrees and participates in the experiment. The transporter therapy begins and they accidentally create a sub-conscious clone.
The khan-blood-augmented Kirk becomes enraged and frustrated by the situation, he overwhelms the security guards and even Spock, and makes a last second decision to escape from the Enterprise.
He goes into exile.
The crew learns that the clone has no conscience and cannot be revived as is. The body is hidden.
Starfleet again demands that Spock and crew must return and face full investigation.
Spock rationalises that it was the uncharacteristic behavior of their Captain that caused the situation of the Klingon's and goes into the pursuit of "Kirk", believing his capture was the key to ending the hostilities...
but the truth was Spock wanted his friend back.