Warning: Spoilers for the recently-released Star Trek: Beyond movie

S3E9: Toxic Humanity

Cold open: Same as in ST:B.

One of the Teenax who attacks Kirk becomes ill after the attack, because human blood is toxic to Teenax. McCoy places Teenax (all the Teenax are called Teenax; they insist that as they speak it, each name is distinct) in stasis but cannot cure it. However, the Fabona (who look like 9' tall sunflower plants) offer a second artifact with healing powers. This time, the Teenax choose to overlook the fact that the artifact may be "stolen" in order to save the life of their countryman.

B plot: Scotty plays a practical joke on Keenser, but its race is unfamiliar with the concept. Keenser takes it in stride, but an attempt to reciprocate the practical joke goes awry.

B2 plot: Kirk's upcoming birthday; subspace communication with Commodore Paris about promotion to a desk job.

S3E10: Starbase Boondoggle

Main plot: Commander Spock learns of the death of Admiral Spock. Nyota prepares Plomeek soup for him, but the gesture enrages Spock who loses control of his emotions for a moment. Nyota forgives him, but Spock decides that he must end his romantic relationship with her and rededicate himself to Vulcan cultural principles and the creation of a New Vulcan. She offers to return the necklace, but he refuses it.

B plot: Billed as the Federation's largest engineering effort to date, Yorktown Station is not all it is hyped to be. Problems range from wonky comms to broken replicators. "At least the gravity stayed on this time!" quips Sulu's partner (whose name we actually learn) when the lights fail during a romantic dinner.

S3E11: Altamid Part 1

More or less follows the movie from Kalara's arrival at Yorktown Station to Krall's "Cut her throat" or maybe the saucer section impact depending on pacing. Makes clear a couple of things in my headcanon, the foremost being that Enterprise only recalled a partial crew for the mission, since it was to be of short duration.

S3E12: Altamid Part 2

More or less follows the movie until Krall's attempted deployment of the bioweapon in Yorktown. Commander Finnegan, who has been dealing with its broken systems for months, knows how to shut down the supposedly failsafe life support system: just change the settings to specify earth-standard atmosphere (21%), instead of the current oxygen-rich (28%) mixture. Krall, trapped in the circulation chamber, commits suicide by alien bioweapon rather than receive Federation "therapy".

As we watch the time-lapse construction of NCC-1701-1, voice overs:

Kirk: That ship is beautiful. Too bad I'll never fly her.
Paris: She's is yours if you want her. Perhaps your promotion was just a glitch in the Yorktown's computers

Spock: [stilted language that he was "illogical" to dump Nyota]
Nyota: If that's an apology, I accept.

(My friend Michael wants me to add: and then they find out the new Enterprise is too big to fit in the passage from the construction dock to space)

Here ends season 3