This paper presents a process-oriented case study of successes and failures in collaborative inquiry. The interactions of pairs were recorded and transcribed while they were engaged in learning activities, mediated by agent-based NetLogo electricity models. Transcripts of learner interactions were coded for engagements in science inquiry. The purpose of this paper is to articulate the dynamics of collaborative science inquiry approach resulting from varied scaffolding and consistent scaffolding in learning activities. Our findings indicate that students under a varied scaffolding approach were more deeply engaged in inquiry process and performed better on model-based explanations.