The series opens on an unidentified Klingon speaking to a large assembly about a coming threat—he speaks of the "lighting of a beacon" and intends to unite the 24 houses of the Klingon race to fight against those whose creed is "we come in peace."
Captain Philippa Georgiou and First Officer Michael Burnham of the USS Shenzhou work secretly on a relatively primitive planet. They use advanced technology to open a well to enable the residents to survive a coming 89-year drought.
On Stardate 1207.3 (Earth time May 11, 2256), the crew investigate a damaged interstellar relay in a binary star system. They discover an unidentified object in a sensor dead zone. As the crew of the Shenzhou cannot get a clear reading due to a scattering field, cautious Kelpien Science Officer Saru advises leaving the area. In spite of the recommendation, First Officer Michael Burnham dons a space suit to investigate personally in spite of the dangerous radiation. Out of contact with her ship due to communication interference, she finds a collection of what appear to be ship-sized sculptures along with a Klingon. When the Klingon motions toward her with a weapon, she strikes back, killing him. Her body damaged by radiation nearly to the point of death, she is beamed back to the ship where, after three hours of uncompleted treatment, she reveals the Klingon threat.
The Klingon assembly holds a memorial service for their dead comrade Rejac whom they call a "torchbearer" and vow revenge.
While Burnham is treated, she has a flashback to her childhood where her foster father Sarek counsels her in her studies of alien cultures. This causes her to awaken and leave treatment prematurely to warn Georgiou and the rest of her crew that she encountered a Klingon. Science Officer Saru suggests that she is confused due to suffering a concussion and tells her to return to the sick bay. Georgiou believes her and locks on weaponry on what turns out to be a cloaked Klingon vessel. It becomes visible and is several times larger than the Shenzhou. Inside the vessel, the Klingons debate attacking the smaller ship and if it is consistent with a prophecy. The leader also reiterates the need to "light the beacon," now referred to as the "Light of Kahless." A light-skinned Klingon volunteers to light the beacon, but is rebuffed by the assumed leader and told that as he doesn't belong to a Great House, he is unworthy for such a task. The light-skinned Klingon assures the leader of his faith and places his hand over an open flame and holds it there, causing severe burns yet leaving the Kingon unfazed. This act seems to change the demeanor of the leader, and he hands over his bat'leth to the the light-skinned Klingon and names him Torchbearer. As this is happening, a report comes in showing movement on long range sensors, which seems to fulfill a prediction made by the leader at an earlier time.
On the Shenzhou, scans of the Klingon flagship show it is covered in the sarcophagi-like coffins. Starfleet orders the ship to hold position and take no action until reinforcements arrive. Captain Georgiou is concerned that Shenzhou is currently the only line of defense between the Klingons and an Andorian colony. An ear-piercing electromagnetic signal abruptly permeates through the ship and causes the crew extreme discomfort until they manage to filter it out. Commander Burnham opens a subspace channel to the Vulcan Sarek. They discuss the unusual behavior of the Klingons and come to the conclusion that some new leader is causing change within the Klingon Empire. Sarek also alludes to a dark incident in Commander Burnham's past. After finishing her conversation with Sarek, Burnham recommends to the Captain that the Shenzhou attack the Klingon ship. She justifies her opinion by pointing out that the Vulcans have used preemptive strikes in the past to meet threats from the Klingons. The Captain and Commander descend into argument about the Federation's ideals and what would be the moral and right course of action in this situation. After Captain Georgiou orders Commander Burnham to stand down, Burnham disables the Captain with a Vulcan nerve pinch. She then takes command of the ship and orders an attack on the Klingon vessel, while lying to the crew about the whereabouts of the Captain. She orders the attack over the objections of Science Officer Saru, but the Captain re-enters the bridge before the attack can be carried out. The ship detects a number of incoming warp signatures, and several large Klingon vessels drop out of warp.