Introduction: HER2-positive breast cancer (BC) represents 15-20% of all BC cases and remains an aggressive subtype due to resistance to HER2-targeted therapies, often leading to metastasis. Understanding the molecular evolution of HER2-positive BC and identifying biomarkers for resistance are crucial for improving therapeutic outcomes. This study investigates MYC amplification, tumour-infiltrating lymphocytes (TILs), and genomic characteristics in HER2-positive BC to better understand resistance mechanisms and inform treatment strategies. Methods: The role of TILs as biomarkers of response was explored using computational techniques to evaluate immune infiltration and its association with clinical response to trastuzumab-containing regimens. A meta-analysis of baseline samples was conducted to identify immune subsets predictive of pathologic complete response (pCR). Whole genome sequencing (WGS) was performed on matched primary, metastatic, and normal-adjacent tissues from non- responders (NRs) to assess copy number alterations (CNA) and mutational signatures. MYC amplification and expression were examined in HER2-positive BC samples across different PAM50 subtypes using genomic, transcriptomic, and proteomic analyses. Results: TIL analysis revealed a statistical association between memory B-cells and pCR, though data heterogeneity limited conclusions. Paired on-treatment analysis demonstrated shifts in immune responses, with lapatinib modifying innate immune responses and dual HER2-targeted therapy affecting both innate and adaptive systems. WGS of NRs revealed a higher CNA burden driven by copy number gains, with chromosome 8 amplifications linked to poorer clinical outcomes. Mutational signature profiling identified signature 30 as the most prevalent, associated with chemotherapy-induced DNA damage, while other signatures (2, 11, 19) were related to APOBEC and DNA damage mechanisms. No significant differences in overall survival (OS) were observed between primary and metastatic samples. Whilst no co-amplification of MYC and HER2 was observed, basal-like BC showed a positive association with MYC across genomic, transcriptomic, and proteomic levels. In-vitro studies validated these findings, suggesting MYC inhibition may be a viable therapeutic strategy for basal-like BC. Conclusions: This study provides insights into the molecular mechanisms driving resistance in HER2-positive BC, highlighting MYC as a potential therapeutic target. These findings underscore the complexity of resistance in HER2-positive BC and provide insights into the genomic and immune characteristics that could guide future treatment strategies.