Episode 1: Aftermath - The Discovery finds itself in the 33rd century, having overshot its destination by a few decades. The ship is in disarray, and much of the crew injured from the battle. Michael's suit ceases to operate, and she is saved from certain death by a last-minute transport. The time crystal is no more.
Episode 2: Pirates - With Stamets still out of commission, Discovery begins the weeks-long journey to Terralysium. The Federation, if it still exists, is long out of communications range, and this part of the Beta Quadrant seems barren of civilizations. Suddenly, pirates attack! The technology is far superior to Discovery's, crippling the already ailing ship, and boarding the ship very soon after commencement. A close battle is fought, with heavy casualties amongst the crew (RIP Dr. Pollard), and at the end of the episode, we find the dark secret: the pirates (all dead) were human.
Episode 3: Terralysium - The ship makes it to its destination, only to find the planet completely abandoned. War had come to Terralysium, and the inhabitants had made it off-world. Some likely going into piracy. No sign of Dr. Burnham or Control, and it's believed that the timeline was reset, and she was lost to the sands of time. Michael ends the episode grieving over her mother.
Episode 4: The Benevolence - Still working on repairing their spore drive, the Discovery meets its first non-aggressive society, the Benevolence. The Benevolence greets them openly and peacefully, and offers to repair their ship and crew. Taking it under advisement, the Benevolence share many details of the 33rd century Beta/Delta corridor, but they lack information on any Federation cultures. Discovery deems the spore drive off-limits, as the Benevolence deems their transwarp off-limits. In a pilot program to prepare some of the crew for Benevolent quick-healing, acting CMO Culber makes a startling discovery: the Benevolence are actually controlled by metallic nanites!
Episode 5: Resist - The Benevolence senses the apprehension from the Discovery, and six crew members are infected by the Benevolent nanites. They are not Control, but the Borg, seeking to understand this ship and its crew, and peacefully add them to their Collective. The Spore Drive is anathema to them, however, and a short battle is ended when Stamets sends the Discovery and the Benevolent Sphere into the mycelial network, where the jahSepp makes short work of them.
Episode 6: Tilly! - Stranded in the mycelial network, the Discovery meets with the jahSepp known as May Ahearn, who is mad at almost 1000 years of loneliness. Tilly makes amends and negotiates safe passage back to Earth on one condition: the destruction of the Tardigrade race. Captain Saru won't stand for such destruction, and is accused by May of hypocrisy after they had destroyed the Benevolent ship and all inhabitants. After much deliberation, the Discovery provides May with a method of tagging and locating tardigrades, utilizing sphere data, with the promise that they won't genocide the creatures. The ship is then deposited outside of Earth.
Episode 7: Pax Galactica - The Federation of All greets the crew of Discovery after a long journey. A multi-species, multi-cultural hive of technology exists on Earth and they were all expecting the Discovery to arrive. Captain Saru is hailed a hero, Commander Burnham offered her own ship to Vulcan. But something's not right. Reno and Nhan go over the records allowed. This Federation is keeping secrets, deep dark ones, buried in their official histories. It turns out, that a Civil War has been brewing, and the Federation was ruled by a cabal of oligarchs. Vulcan has rebelled, Andoria has fallen, and the colony worlds cut off and attacked. Stamets is kidnapped by the oligarchs, who only want the key to time travel, a lost technology, and the sphere data. A last minute rescue by Nhan results in Discovery jumping as far away as it can go.
Episode 8: Where the Sirens Dwell - Discovery has travelled beyond all known galaxies, into a place believed to be near the edge of the universe, if such a place could exist. Illusions appear: Burnham sees her parents, Saru sees his sister, Detmer sees that guy she mentioned that one time. It's all very confusing and weird. The hallucinations cause discord amongst the surviving crew, but Reno, ignoring her dead wife, straps an unconscious Stamets into the spore drive and they head to Boreth.
Episode 9: The Promise - Boreth remains unchanged. Despite lying deep within an expanded Gorn Hegemony, the surviving Klingons have managed to keep their world closed off from outsiders. Saru and Burnham fail to make a plea, and a Gorn Armada prevents anyone from beaming down. Knowing a thing or two about Gorn, Specialist Georgiou manages to beam a strike team on their main ship and order Boreth to allow beam-ins on principle. Georgiou and Nhan beam to the monastery and receive an audience with Tenavik, who has not aged a day. Unfortunately, only one time crystal remains. And they are not worthy of it.
Episode 10: Chrysalis - Going against Saru's order, Georgiou and Nhan fight through the monastery to get the last crystal. These Klingons are strong, and masters of illusion it seems. Tenavik knows all their moves before they make it, and Saru and Burnham beam down to diffuse the situation. In the end, Georgiou manages to gain the last time crystal, but is paralyzed by Tenavik in a bubble gun. For breaking the laws of time, she and the crew, the entire crew, of the USS Discovery must do penance on Boreth. The ship vanishes to parts unknown, as the Gorn and Klingons beam their prisoners down to the monastery.
Episode 11: No Time Like the Present - After several years of penance, Gabrielle Burnham appears to Michael in her cell at night. Turns out she's alive and coming to rescue Michael and bring her to the 23rd century. Michael refuses to go without her crew, but Gabrielle can only take one. A convoluted plan is hatched, involving sending Owo back with the understanding that she will have a stasis ship ready and set to rescue them, but Georgiou complicates matters by mixing up Owo's DNA sample with her own, so only Georgiou can use Gabrielle's suit to travel to the past. She leaves promising to send the cavalry.
Episode 12: The Cavalry - Georgiou is in 2259, where she must inform Starfleet all that has transpired. They lock her up for Control's crimes, all blamed on her introducing an invasive program in order to wipe out the Federation and take over. Captain Pike doesn't buy any of it, and uses his contact with Commander Tyler to get her out of a secret Section 31 prison. She tells him the plan, and they begin plotting the best course of action to prepare a well-armed stasis ship for a journey of a thousand years. Their requisition doesn't work, mainly due to the interference of Commander Mendez, Tyler's rival, who is tasked with hunting down and killing Georgiou to protect from temporal interference. Pike and Georgiou's stasis ship is shot down by Mendez before it can launch, but a battle is prevented by the unexpected arrival of an abandoned Discovery.
Episode 13: Unexpected Discovery - Tyler, Mendez, Georgiou, Spock, and Pike explore the abandoned Discovery and Georgiou informs them of where it arrived from. Spock determines the ship to be over a thousand years old, travelling in isolation the same distance backwards as it would be forwards. Remnants of Control have taken over the ship, and has seperated the crew from each other as it warps away. Spock is infected with the nanites, as the Enterprise, under Una's command, pursues the ship. Pike and Georgiou develop a countermeasure to Spock's infection, as Mendez is presumed killed. Finding Benevolent nanites in Culber's test lab, Georgiou reconfigures them to fight Control on a microscopic level within Spock's body (Spock is quarantined in the spore chamber), causing much physical torment that would kill a normal human. The Sphere Data, having evolved itself an AI personality, fights Control within itself, as parts of the ship power on and off, lights flicker, and Discovery even torpedoes itself. Finally, Georgiou gives the Sphere AI full access to all ship functions, and it immobilizes and destroys the Control remnant. Mendez is resurrected with Benevolent nanites, and no memory of the events, as Pike programs the ship its new destination of Boreth in 1000 years, and wishes "Zora," named for his mother, godspeed on her journey.
Episode 14: The Klingon Redemption - Zora arrives, the long way, at Boreth in a 1000 years, and begins the process of fighting the Gorn Armada. Zora has examined technology of the period, as well as access to technology from 100,000 years of galactic history, and is more than capable of besting the Gorn. But, Tenavik and the monks of Boreth open up a time tsunami to swallow the ship and planet. Tenavik, though, is a turncoat, and decides to save the ship and crew. He gives them the last time crystal. He is killed by a rival monk, played by Michael Dorn, but its too late, and Zora transports them to the ship and they leave Boreth. Weeks later, they contemplate their next move when Gabrielle appears to Michael and informs them of a dire threat to all of time and space itself: the jahSepp have declared war on the universe, and are in the process of devouring the Big Bang.