The fourth act of this film is by far the shortest. Barely the last 20 minutes of the film, we return to the 23rd century and hope to release our whales. While it's easy to think of this only as an action sequence, it does resolve an important plot since the end of Star Trek 2.
Earlier in the film, McCoy questioned Spock's capabilities to Kirk, and even asked for his confidence in our favorite Vulcan. Kirk didn't answer, but his silence spoke volumes.