HCV develops a chronic infection in humans, which ultimately leads to liver failure. Discovery of direct-acting antivirals (DAAs) has initiated the era of well tolerated medications. While these treatments are useful but still encounter certain limitations including drug resistance mutations, selective immune pressure and various side effects. Besides, no effective vaccine for the prevention of HCV infection is yet available. Therefore, for the development of efficient antiviral treatment, comprehensive knowledge of viral proteins characterization and pathogenesis is essential. The current study attempted to use integrated approaches to characterize the HCV major drug target proteins NS3/4A, NS5A and NS5B. Here, we provide a detailed analysis of the drug and immune driven variations among these viral proteins using systems virology and proposed a mechanistic insight highlighting the importance of these mutations on the therapeutic and immune response. In NS3/4A, DRMs such as A36V, Q80K, M175L, I132L, S138T, and R123T were observed in epitopes associated with HLAB*57, HLA-B*27, DRBl*ll04, and DRB1*0101 alleles. Within NS5A, DRMs such as L31M, Q30K/R, L28V, F28L, Q54H, and H58P were found in epitopes related to DRB1*0701, DRBl*ll04, HLA-A*68, and DRB1*0101 alleles. Similarly, DRMs including D168V, M423I, M419M, V494A, V499A, V138I, and I482T were frequently found in epitopes associated with DRB1*0101, DRB1*0701, HLA-B*57, HLAB*27, and DRB1*1104 alleles within NS5B. Among these alleles DRB1*0701, DQA*0201,DRBl*ll04, DRB1*0101, DRB*5701, DRB*5703, Cw*0102, DQBl*O301, HLA-B*57, HLA-A*03, HLA-A*68, and HLA B*27 are involved in HCV protection or clearance. Moreover, the efficacy of four prioritized drugs with no drug and immune driven variations, Danoprevir, Balaprivir, Narlaprevir, Samatasvir was compared with Sofosbuvir using in vitro analysis and highlight the significance of these drugs as more efficacious and potential therapeutic targets. This study also attempted to investigate the evolutionary conservation of these proteins (NS3/4A, NS5A and NS5B) via global consensus sequence profiling of all HCV genotypes (Thio et al.). This comprehensive analysis finds out many conserved drug targets and post translational modification sites (PTMs) that could be a target for the development of universal drug and vaccine. This study also aimed to propose a conserved pan genotypic multi-epitope vaccine by using structural modeling and epitope-epitope compatibility as a promising strategy to combat HCV infections, effectively. Multi-epitope vaccine construct was designed by using sixteen linear conserved epitopes, to induce better antigenic responses than a univalent subunit vaccine. Thus, surface-exposed, conserved and antigenic epitopes from the selected viral proteins were screened to design broad spectrum multi-epitope based subunit vaccines. While stable and substantial interactions were also observed with Toll-like receptor 3 and 8. This study showed that integrated lines offer various opportunities to amass the incomplete mystery of HCV biology in a meaningful way. It will increase our comprehension of how HCV roots liver diseases and how different hidden an unanticipated mechanism including immune driven variations could affect its therapeutic response. It also provides efficient screening stratagem to effectively extract worthwhile insights from multidimensional molecular datasets and helps in improving our understanding of the development of possible therapeutic targets against HCV