Complex sentence: Misato has Toji and Kensuke take cover in Unit 01's entry plug before ordering Shinji to retreat, but he disobeys and destroys the fifth Angel with Unit 01's Progressive Knife.
Split into simpler sentences: Misato has Toji and Kensuke take cover in Unit 01's entry plug before ordering Shinji to retreat. However, Shinji disobeys and destroys the fifth Angel with Unit 01's Progressive Knife.