The study aims to evaluate the effectiveness of an inquiry-based virtual reality (VR) science lab used in junior high school science classes. The "Scientific Investigation VR Lab" ("SIVRLAB") is designed for 9th-grade students to learn about electrochemical cells. It is situated in a guided problem-solving context, where learners need to review the concept of oxidation-reduction reactions and assemble a voltaic cell to save a robot. The "SIVRLAB" features several cognitive supports and guides for students to plan and record experiments and resolve the problem. It has both a head-mounted display (HMD) version and a desktop VR version. The study recruited 66 9th graders from three classes to evaluate the two versions of the "SIVRLAB." The students were assigned to one of three conditions, namely, (1) using immersive HMD "SIVRLAB" individually, (2) using desktop "SIVRLAB" individually, and (3) observing one student use immersive HMD "SIVRLAB." The students were briefly introduced to the concept of electrochemical cells in the first class and were instructed to use the "SIVRLAB" sessions in the next class. The results from knowledge pre- and post-tests, a user experience survey, and students' reflections were collected and analyzed qualitatively. The findings revealed that students who used the desktop VR obtained the highest test scores among the three groups. However, in the follow-up physical laboratory test, the performance of the students in the original HMD VR experimental group was better than those in the desktop VR experimental group. The paper also discusses student feedback and teacher observations regarding the design and interaction with immersive VR. Lastly, the implications of the study and recommendations for future studies are presented.