Manipulatives aim at assisting human not only to accomplish certain tasks but also to enhance cognitive development. Teaching and learning with use of manipulatives are evolving in response to new trends of pedagogy. Interactive learning environment particularly in tool-based context, is conceived so that students develop high-order thinking with manipulation with tools.This paper presents a part of a research project investigating teaching and learning with use of tools contextualised in a series of mathematics lessons conducted in a science laboratory. An intrinsic case study focusing on implementation of the apparatuses-based mathematics lessons, is being reported. A tool-based problem, designed by an experienced science teacher from a secondary school, associated with inclusion of apparatuses emerged in science laboratory, is formulated to foster students’ cognitive development of mathematics knowledge specifying in estimation. Five series of lessons were video-recorded and transcribed. Pre- and post- lessons interviews with teacher and students were conducted to collect teacher’s perception of tasks designed for the lessons which was triangulated by viewpoints of students. Didactical cycle framed in tool of semiotic mediation is adopted as one of the main analytical frameworks to examine protocol of teaching trajectory in the series of the lessons. Teacher’s didactic and students’ pragmatic manipulations with the apparatuses were being prominently considered to demystify implementation of the lessons while teaching flows as well as evolution of signs associated with involvement of the tools were captured and analysed in the study.The findings of the study illustrate didactical interactions which is a modified framework yielding reverse transitions of activity phases stated in didactical cycle. Enhancement of interactive activity phases based on analytical frameworks provides empirical evidence to contribute to pragmatic didactics with uses of apparatuses. In addition, its findings disseminate integration of epistemological contents of mathematics, science and technology which devote to STEM education.