The girl who died was Kyla and this happened in episode 10 of season 2 "Skinwalker".
Summary from
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(they have good summaries and reviews for SV)
"Skinwalkers"
Story By: Mark Warshaw
Teleplay By: Brian Peterson & Kelly Souders
Directed By: Marita Grabiak
Produced By: Bob Hargrove
Aired in the U.S.A.: 11.26.02
Roles & Actors this episode:
Clark Kent: Tom Welling
Jonathan Kent: John Schneider
Martha Kent: Annette O'Toole
Lana Lang: Kristen Kreuk
Lex Luthor: Michael Rosenbaum
Lionel Luthor: John Glover
Ian Randall: Jonathan Taylor Thomas
Pete Ross: Sam Jones III
Henry Small: Patrick Cassidy
Chloe Sullivan: Allison Mack
Mr. Sullivan: Robert Wisden
Joseph Willowbrook: Gordon Tootoosis
Kyla Willowbrook: Tamara Feldman
At a site where Luthorcorp is building a new office park, the men are done with their day's work and are leaving for the day. But when the foreman goes to lock the gate he finds Joseph Willowbrook, a local Indian activist, inside protesting the fact that the office site's being built on his people's sacred ground. The foreman tells him to leave but Joseph warns him of unknown forces at work before he goes. That night the foreman is gassing up his truck on the site when a huge white wolf attacks him! Grabbing a flare gun he fires at the wolf but the shot is deflected into gas that's leaked on the ground and the ensuing explosion kills the poor man!
While Pete Ross and Clark are motocrossing near the construction site the next day, they don't know that danger lies undeneath them. When Clark takes a spill, he suddenly plummets 100 feet down into a huge cave. A chamber is opened from another area by Clark's fall, and a pretty young Indian girl runs to Clark's side to preform first aid on him, but his amazing body has once again saved him from harm. The young lady is named Kyla and she is the grandaughter of the Indian who was protesting the offices being built. Then the pair notice the walls covered in ancient drawings of what Kyla says is the legend of "Numan" who came from the stars and shoots fire from his eyes while having the strength of ten!
Pete calls down but since Clark is all right he and Kyla continue looking over the caves under the work site. Then Clark notices to his amazement an indentation carved into the wall in the exact shape of the octagonal disk that fits into his spaceship's side and will activate it. Now he is very interested in this legend and meanwhile he and Kyla are also instantly attracted to each other. Later at home Clark tries to get his Mother to talk Lionel Luthor out of developing the site further as the caves have been discovered, but she tells Clark she doesn't have any say in Luthorcorp.
Kyla stops by Clark's barn to talk and the two become even more enamored with each other. Kyla is wearing a bracelet in the shape of a symbol in the cave and she tells Clark that once there was a great star in the sky where "Numan" came from. Lana stops by and meets Kyla and Clark asks her to ask Henry Small, a local lawyer and the man who may indeed be Lana's biological Father, to intercede on the Indian's behalf, and Lana agrees reluctantly. Lex's father asks Lex to come into the office project as his partner and Lex refuses to do any business with him.
When Clark and Kyla re-examine the cave paintings, a sudden cave-in from the bulldozers working above almost hurts Kyla. But Clark sheilds her with his body which she is amazed at and now Kyla is convinced Clark is the legend called "Numan"! The two share a kiss in the cave that cements their feelings towards each other even more. Lana meets Henry Small at the Talon coffeeshop and he tells her he'll be glad to help the Indians fight Luthorcorp. He then also tells her the DNA tests are back and he is her Father after all! He also wants to start a relationship with Lana where he can learn to be a real father to her which makes Lana very happy. Clark finds out that Joseph Willowbrook has been arrested for suspicion about the foreman's death, and he asks Lex to bail the man out of jail. Also Henry Small files a "Cease and Desist" order which stops construction at the office park site. Lana tells Chloe that she's been writing to Whitney in the service regularly but lately he stopped answering her letters to him. When Clark takes Lex to the caves and he also sees the indentation for the spaceship in the form of the disk stolen from him, he becomes a solid backer of the Indian's cause and bails out Mr. Willowbrook.
That night as she's leaving work, Martha Kent is attacked by the huge white wolf as she enters her car but she escapes any injury. Lex tells his Father he'll take the office site project off his hands but his father becomes wary of Lex's sudden interest in the caves and refuses Lex's offer. That night Kyla tells Clark her tribe name means "Skinwalkers", actual people of her tribe who were exposed to green stones and were given the power to change into animals. When Clark asks Kyla if her grandfather could actually be the huge white wolf involved in the murder, Kyla feels hurt and leaves. Later that night Lionel Luthor is home in his mansion when he hears a huge wolf growling outside and trying to get into the room!
The massive beast breaks into the room and the blind Luthor is seconds away from a violent death when Clark bursts into the room just ahead of Luthor's security guards. He stops the men from shooting the wolf and asks it to leave peacefully which the wolf then does. But as the wolf's jumping out the window, it cuts itself badly on the glass and falls to the ground mortally wounded. Clark leaps down expecting to find Jospeh Willowbrook is the wolf, but he is shocked to see Kyla lying there bleeding to death! She tells Clark she's a "Skinwalker" and she never intended to hurt the foreman or his mother when she turned into the wolf, she was just trying to save her people's heritage. She tells Clark she's sorry and then passes away in his arms as he weeps for her.
It turns out the state invokes an historical preservation law which takes the project away from Luthorcorp. And Lex brags to his father that it's his company Lexcorp that has won the contract for the excavation of the Indian site. But Lionel Luthor tells his son he knows that Lex has found something he values on the site and he intends to find out just what it is in the near future. Later that night Lana consoles Clark about Kyla and then she collapses in his arms in tears. When Clark asks what's wrong, she tells him she's gotten word that Whitney has been listed as "Missing In Action" by the Marines. As Clark holds his crying friend he has little time to mourn for his own loss, the young and beautiful Kyla.