The study presents three cryo-electron microscopy (cryo-EM) structures of the complete Integrator–PP2A complex in different functional states, revealing the structural basis of Integrator-dependent RNA polymerase II (Pol II) termination. The pre-termination complex structure shows a previously unresolved scorpion-tail-shaped INTS10–INTS13–INTS14–INTS15 module that may use its 'sting' to open the DSIF DNA clamp and facilitate termination. The post-termination complex structure shows that the previously unresolved subunit INTS3 and associated sensor of single-stranded DNA complex (SOSS) factors prevent Pol II rebinding to Integrator after termination. The free Integrator–PP2A complex structure reveals that INTS6 blocks the PP2A phosphatase active site. These results lead to a model for how Integrator terminates Pol II transcription in three steps involving major rearrangements. Integrator is a 1.5-MDa complex that regulates Pol II transcription by terminating transcription at promoter-proximal regions. The Integrator complex binds to the paused elongation complex (PEC) consisting of Pol II, DSIF, and NELF, and cleaves the nascent RNA transcript. The Integrator cleavage module contains endonuclease activity and resembles the cleavage module of the cleavage and polyadenylation specific factor (CPSF). The Integrator cleavage module docks at the RNA exit tunnel of Pol II such that the exiting nascent RNA would proceed directly into the endonuclease active site for cleavage when Integrator binds to the PEC. The roles of the flexible Integrator subunits and the SOSS factors in Integrator function are unclear at the molecular level. Integrator-dependent Pol II termination is thought to occur in three steps. First, Integrator binds to the PEC and the phosphatase activity of the Integrator-associated PP2A dephosphorylates the Pol II CTD and the C-terminal region of the DSIF subunit SPT5. Second, the endonuclease activity in INTS11 cleaves the exiting nascent RNA, generating an uncapped RNA 5' end. The third and final step requires the unravelling of the DNA–RNA hybrid and the release of the DNA that is locked in the Pol II cleft by two clamps—the Pol II clamp and the DSIF DNA clamp. The study reports three cryo-EM structures that show previously unresolved Integrator subunits and the Integrator-associated SOSS factors. Together, these structures provide insights into how Integrator terminates Pol II, leading to a dynamic model for Integrator action.The study presents three cryo-electron microscopy (cryo-EM) structures of the complete Integrator–PP2A complex in different functional states, revealing the structural basis of Integrator-dependent RNA polymerase II (Pol II) termination. The pre-termination complex structure shows a previously unresolved scorpion-tail-shaped INTS10–INTS13–INTS14–INTS15 module that may use its 'sting' to open the DSIF DNA clamp and facilitate termination. The post-termination complex structure shows that the previously unresolved subunit INTS3 and associated sensor of single-stranded DNA complex (SOSS) factors prevent Pol II rebinding to Integrator after termination. The free Integrator–PP2A complex structure reveals that INTS6 blocks the PP2A phosphatase active site. These results lead to a model for how Integrator terminates Pol II transcription in three steps involving major rearrangements. Integrator is a 1.5-MDa complex that regulates Pol II transcription by terminating transcription at promoter-proximal regions. The Integrator complex binds to the paused elongation complex (PEC) consisting of Pol II, DSIF, and NELF, and cleaves the nascent RNA transcript. The Integrator cleavage module contains endonuclease activity and resembles the cleavage module of the cleavage and polyadenylation specific factor (CPSF). The Integrator cleavage module docks at the RNA exit tunnel of Pol II such that the exiting nascent RNA would proceed directly into the endonuclease active site for cleavage when Integrator binds to the PEC. The roles of the flexible Integrator subunits and the SOSS factors in Integrator function are unclear at the molecular level. Integrator-dependent Pol II termination is thought to occur in three steps. First, Integrator binds to the PEC and the phosphatase activity of the Integrator-associated PP2A dephosphorylates the Pol II CTD and the C-terminal region of the DSIF subunit SPT5. Second, the endonuclease activity in INTS11 cleaves the exiting nascent RNA, generating an uncapped RNA 5' end. The third and final step requires the unravelling of the DNA–RNA hybrid and the release of the DNA that is locked in the Pol II cleft by two clamps—the Pol II clamp and the DSIF DNA clamp. The study reports three cryo-EM structures that show previously unresolved Integrator subunits and the Integrator-associated SOSS factors. Together, these structures provide insights into how Integrator terminates Pol II, leading to a dynamic model for Integrator action.