In Season 3 Episode 2 of His Dark Materials (The Break), from the clue that Lyra is with her mother as obtained from Fra Pavel Rasek's Golden Compass, Gomez uses spy magic to locate Marisa Coulter's location and brings his soldiers on spaceships to Germany.
Angel Balthamos on his way back to the Republican base is intercepted by angel Alarbus, who is loyal to the Authority. Both fall to the ground at the base; Balthamos dies after informing Asriel of the news on Will and Lyra. Alarbus is imprisoned and tortured by Asriel with his Dust-powered machine to reveal information about the Authority, who remains hidden and governs through a Regent.
Will finds Marisa Coulter's stone house and is completely convinced that Lyra is safe with her mother. Marisa Coulter tries to keep Will stay because he has the powerful knife which is believed to protect her and Lyra. however Will insists on going to Asriel's base. Just as Will is about to leave the island, Gomez's spaceships arrive.
Marisa Coulter apply some tricks to cheat Gomez but fails, eventually she teams up with her deamon to knock Gomez unconscious (or dead posssibly). At this point Will returns and takes Lyra away, but Marisa Coulter tries to stop them. As Will is cutting the portal to the other world, Marisa Coulter keeps talking about how Will had abandoned his mother, making it impossible for him to concentrate, leading to breaking the knife into pieces.
Asriel's tiny spy attacks Marisa Coulter unconscious, allowing Will and Lyra to escape through a portal he cut earlier.
In Season 3 Episode 1 of His Dark Materials (The Enchanted Sleeper), Lord Asriel Belacqua journeys to another world to recruit Commander Ogunwe into the forces of the Republic of Heaven in the war against the Authority; Meanwhile, Marisa Coulter takes Lyra to an island in Germany to avoid the hunt of the Magisterium, and gives her daily anesthetics to fall into a deep sleep.
With the help of the subtle knife Æsahættr, Will travels through many worlds in search of Lyra but to no avail because he has no clue to where she could be.
He meets two angels, Baruch and Balthamos, who want to bring him to join Asriel's forces. Balthamos uses the Golden Compass to help Will locate Lyra, after which he returns to Asriel's base to report the news. Baruch goes with Will to find Lyra.
Along the way, Will encounters Iorek Byrnison the Bear who is raiding a village demanding the release of another bear. Will empowers Iorek and asks the villagers to release the captured bear. Iorek joins Will on a journey to find Lyra.
In Geneva, believing that Lyra was the embodiment of Eve - the mother of all sins, Cardinal Hugh MacPhail sent Father Gomez to lead a force to capture Lyra and Marisa Coulter.
In Episode 6 of His Dark Materials, Mother, after being captured, Lyra is taken to the Bolvangar base where children are cut away from their daemons in a radiation machine. She meets her friend Roger there and they make a plan to escape, a long with other imprisoned children.
Before she can carry out the escape plan, she is taken to the laboratory to cut her daemon Pan way. She screams for help, and calls out "Mother" to Mrs. Coulter who is in a visit to the base. Mrs. Coulter saves her, they exchange a moving story about their feeling in the mother-daughter relationship. However, she askes Lyra to choose a side between her and Lord Asriel. Lyra plays a trick to run away from Mrs. Coulter, then turns the Bolvangar base into ruins by damaging the radiation machine. Gyptian people, along with bear Iorek, witch Serafina and Dr. Lee just show up in time to defeat the base's armed men and liberate all the children. Then Lee helps bringing Lyra, along with Iorek, on his balloon ship flying further north to find and save Lord Asriel. On the way, they are attacked by cliff-ghasts (similar to flying monkey), Lyra is tossed down from the ship.