Five years after the end of the Clone Wars and the rise of the Galactic Empire, former Jedi Padawan Cal Kestis is living in hiding on the planet Bracca, disguised as part of a work crew breaking up derelict ships from the war for scrap metal. While dismantling the wreckage of a Republic warship, an industrial accident drives Cal to use the Force to save his co-worker and friend Prauf from falling to his death, despite the presence of an Imperial probe droid. In the aftermath, Prauf advises Cal to leave Bracca before he's discovered, but their train is raided by stormtroopers led by two Imperial Inquisitors, the Second Sister and the Ninth Sister. Prauf sacrifices himself to buy Cal time to flee, and Cal is rescued from being killed by the Second Sister by the crew of the Stinger Mantis; former Jedi Knight Cere Junda and Lateron pilot Greez Dritus.
Cere takes Cal to the planet Bogano, in the Outer Rim, where she explains her late Master, Eno Cordova, hid a Jedi holocron on Bogano, containing a list of all Force-sensitive children in the galaxy that could be used to rebuild the Jedi Order. Since Cere lost her connection to the Force during the Jedi Purge, she needs Cal's help to unlock the vault. With the help of BD-1, a droid Cordova left behind to help any Jedi searching for the holocron, Cal learns that Cordova hid clues on how to unlock the vault in tombs built by the Zeffo, a prehistoric race of Force wielders, to house the remains of their greatest sages. The Mantis crew head to the Zeffo homeworld, where Cal learns that Cordova hid another artefact to open the vault on the Wookie homeworld of Kashyyyk with the help of Tarrful, a Wookie chieftain currently leading a rebellion against the Empire. Cal and his companions travel to Kashyyyk, where they help Saw Gerrera and his Partisans, along with the local Wookie resistance, free prisoners from an Imperial slave labour camp, in exchange for Gerrera arranging a meeting with Tarrful.
Since Tarrful cannot be reached at that time, Cal returns to Zeffo after learning the Empire are excavating another tomb there. During his search, Cal is ambushed by the Second Sister; Cal is beaten in battle, but BD-1 saves him by activating an energy shield that cuts off the Second Sister from pursuing. The Second Sister reveals her identity as Trilla Suduri, Cere's former Padawan; Trilla was caught by the Empire when Cere betrayed her hiding place under torture during Order 66, and tortured into becoming an Inquisitor. Trilla warns Cal that Cere used the Dark Side of the Force to escape captivity, and that she will betray Cal as well. Leaving Trilla behind, Cal discovers too late she has already looted the artefact the Zeffo tomb contained, and en route back to the surface, he is ambushed by bounty hunters working for the Haxion Brood, a crime syndicate that Greez owes money to. Held captive at the Brood's lair in an asteroid belt, Cal is forced to fight in a series of gladiatorial games against various beasts and combat droids until Cere and Greez crash the Stinger Mantis into the base to rescue Cal. After they escape, Cal confronts Cere about Trilla's accusations; Cere reluctantly confesses that during Order 66, she was captured while trying to lead clone troopers away from the hiding place of Trilla and several younglings they were protecting and tortured into giving up their location. The realisation Trilla was telling the truth sours the relationship between Cal and Cere.
After receiving a communication that Tarrful wants to meet, Cal returns to Kashyyyk; Tarrful advises Cal to look for more information at the top of the Origin Tree, a sacred site in Wookie culture. Under attack from Imperial forces led by the Ninth Sister, Cal reaches the top of the tree with the aid of the Shyyyo Bird, the tree's guardian, where he learns an artefact known as an Astrium is required to unlock the Bogano vault, and that one can be found on the planet Dathomir. The Ninth Sister tries to kill Cal, but he defeats her in a lightsaber duel, severing her sword hand before flinging the Ninth Sister seemingly to her death from the top of the tree.
En route to Dathomir, at Greez' urging, Cal buries the hatchet with Cere and agrees to focus on the future, rather than the past, and he accepts Cere is trying to make amends for her past errors. On Dathomir, Cal makes his way to the Zeffo tomb, fending off attacks by both the indiginous wildlife and the local tribes of Nightbrother warriors, along with their leader, the Nightsister witch, Merrin. Outside the tomb, Cal is accosted by a strange old man, who warns him the tomb and the planet is saturated in the Dark Side of the Force. Inside the tomb, Cal has a flashback to his master, Jaro Tapal, sacrificing himself to save Cal from the clones when Order 66 was executed, as well as facing an apparition of Tapal denouncing Cal as a failure and a false Jedi. Cal unconsciously destroys his lightsaber fending off the apparition, and exits the tomb disheartened. Outside, the old man identifies himself as Taron Malicos, a former Jedi who survived Order 66 but ended up marooned on Dathomir; Malicos offers to teach Cal how to use the Dark Side of the Force, but Merrin appears, accuses Malicos of breaking their alliance and reanimates the corpses of her fellow Nightsisters to attack them. While Malicos fends off the undead, Cal flees back to the Mantis.
With his lightsaber destroyed, Cere takes Cal to the planet Ilum, where the Jedi used to mine kyber crystals to power their lightsabers, to make a new one. Facing the challenges within the planet's cave, Cal nearly succumbs to despair, but BD-1 plays a recording of Cordova that motivates Cal not to give up. Creating a new lightsaber, Cal then fights his way back to the Mantis through the Imperial forces stationed on Ilum, and returns to Dathomir, where he overcomes his guilt and regret over Tapal's death. Merrin, impressed by Cal's honesty and sincerity, allows him to enter the tomb; Malicos again tries to convince Cal to join him and turn to the Dark Side, but Cal refuses and fights him, defeating Malicos with Merrin's aid. Cal recovers the Astrium and returns to the Mantis with Merrin, who agrees to accompany them, wishing to find answers about who orchestrated the destruction of her fellow Nightsisters during the Clone Wars.
Returning to Bogano, Cal unlocks the vault, but receives a vision from the Force warning that attempting to use the Holocron to rebuild the Jedi will end in disaster, with the Empire finding him and his students. Before he can claim the holocron, Trilla attacks him, having followed them to Bogano; when Cal disarms her, touching her lightsaber causes Cal to see the torture she went through at the Empire's hands, allowing Trilla to steal the holocron and escape. Once Cal recovers, he fights off the stormtroopers Trilla brought with her and informs the others of the theft. Cere concludes that Trilla has likely taken the holocron to Fortress Inquisitorius, the lair of the Inquisitors and the place where she and Trilla were held prisoner, on the oceanic moon of Nur, above the planet Mustafar, and they make a plan to recover the holocron. Before assaulting the fortress, Cere grants Cal the rank of Jedi Knight.
Cal and Cere drop from orbit and infiltrate the fortress; while Cere distracts the guards, Cal makes his way to the heart of the fortress, where the holocron is being kept. Trilla attacks him again, but this time, Cal is able to defeat her. Cere reaches them and tries to reconcile with Trilla, but Darth Vader intervenes and kills Trilla for failing him. Unable to defeat Vader, Cal smashes a window that allows the fortress to flood, and Cal and Cere escape while Vader holds back the ocean, Merrin using her magic to save them from drowning.
Back aboard the Mantis, Cal destroys the holocron, having realised that gathering the children it lists would just make them targets to be killed or enslaved by the Empire, and decides to leave their fate to the will of the Force. Their mission complete, the crew ponder their next mission.
