Computer-supported collaborative learning (CSCL) is a technology-driven inquiry-based approach that encourages social interaction and shared knowledge construction in completing computer-aided tasks. Although there were researches carried out on CSCL, no research to date has extensively examined how CSCL enhanced with scripts containing student-generated questions can facilitate the development of logical thinking, an essential skill to effectively comprehend science concepts. In this light, this research examined the effects of co-creating scripts in CSCL on students' logical thinking. This utilized a three-group pretest-posttest quasi-experimental design with two delayed posttests which involved Grade 7 students. One group was exposed to CSCL with scripting while the other group was exposed to CSCL without scripting. On the other hand, the control group was exposed to a conventional teaching approach. Findings revealed that CSCL approaches significantly improved students' logical thinking, F(2, 113) = 5.616, p = 0.0025. Further, the delayed posttests consistently showed that CSCL with scripting significantly influenced the development of logical thinking. Notably, this research builds and extends on previous researches regarding the synergistic scaffolding of the inquiry-based approach, technology integration, collaborative learning, and question-asking activity. This innovation catalyzed learning and offered essential implications that provided opportunities for future research directions.