In Season 3 Shax killed Prue 由 throwing her through the 墙 after she tried to save Dr.Griffith. Piper and Prue were both thrown back into the 墙 to save Dr. Griffith but Leo came back to save them and before that. Phoebe was in the 黑夜传说 with Cole and Leo. Phoebe asked the 来源 to call Tempus to turn back time but it was to late when they got back to save Piper and prue. Leo came back to save Piper and Prue the 秒 time and saved Piper but not Prue because she was already dead.
In season the season 3 finale, prue,piper and phoebe couldn't stop shacks, (please not that this is towarads the END of the episode) shacks died but he had killed prue.
prue died 由 a lighting blast thrown through an 墙 由 the sources assistant shax in theseason 3 finale episode all hells breaks loose and her funeral was shown in the 4th season premiere two parter episodes 圣女魔咒 again part 1 and 2
In the last episode on season 3 (all hell breaks loose) Prue and Piper are injured 由 Shax, a personal assassin for the Source. Leo can only heal one so he naturally chooses Piper, his wife. So in summary she was murdered 由 Shax. In reality she kept causing fights between the 女演员 who play Piper and Phoebe so everyone got sick of his and they threw her off.