This study delved into the “journey” of the Ati as they traverse from their own way of explaining nature, their indigenous way of life, to a multicultural classroom, where science is taught more systematically. This study employed the qualitative research design, where the stories exemplify the dilemmas encountered by the Ati and how this indigenous knowledge can reconcile with what science taught in school. Furthermore, it provided a documentation and analysis of the ethnography of the Ati community, at the context of the school where the subjects of the study are enrolled, the Magayon School. Using the memory-banking technique, the researcher identified the indigenous experiences of the subjects. Concepts were then identified through memory-banking and concept-mapping. Through observation and interviews, it was then identified where these indigenous science concepts were applied. Interviews and Focused Group Discussions (FGDs) were then used to identify border crossings and the dilemmas encountered. Data analysis techniques included thematic analysis, horizontalization, and triangulation methods. Analysis of the results, revealed that the Ati have their own set of indigenous science. Majority of the respondents admitted that they are shy to mingle with non-Ati groups. As a result, they tend to be always with their Ati peers. The FGDs of the participants further revealed that the participants struggle for space within the society, where people would not „put labels on them. It was found out that these reactions tend to have positive or negative impacts of the Atis learning in school. Moreover, the study also reflected that the Ati appreciate the fact that their own indigenous ways are recognized by the school where they study. Seven of the nine respondents described science as difficult and reasons for these were: difficulty in understanding the medium of instruction, the dilemmas encountered, and the lack of interest in the subject. As to classroom instruction, they are open to learn using English as medium of instruction, yet they appreciate the lesson well when they understood it in their own terms. They also hope that being in school may change other people’s perception of them. It is likewise important to consider bilingual programs and native dialects to address the problems of transmission of learning using only one medium of instruction. Some respondents positive perception of science enables them to do well in class. However, some of the respondents admitted that they have difficulties in the subject; this depends on their motivation to schooling. Still others find their school science enjoyable only when they are grouped with their fellow Ati; as a result, they do not mingle with non-Ati groups very well. Such findings indicate that student interest and attitudes are critical aspects of science education.