Traditional plagiarism checkers are built around verbatim string and n-gram matching, which do not account for paraphrasing and other forms of semantic rewriting, making research integrity screening susceptible to bypassing. This paper introduces an enhanced research paper plagiarism detection system implemented in Python, Flask, PyMuPDF, Scikit-learn, and Sentence Transformers. The tool is designed to address the mentioned limitations by utilising a two-step approach that integrates a Lexical Similarity Engine (TF-IDF and cosine similarity) and a Deep Semantic Engine (SBERT paraphrase-MiniLM-L3-v2, with 384-dimensional embeddings). By combining the outputs of both engines, the system calculates a composite plagiarism score, a Research Integrity Index score, and implements a tiered risk classification. Additionally, the tool offers four key features that distinguish it from commercial alternatives, including section-wise analytics, a sentence highlighter, a citation-aware filtering module, and an institutional-level analytics dashboard. An instrumented end-to-end pipeline utilised a 42-paper corpus to demonstrate the system’s applicability. The results showed that all six pipeline stages took a median of 260 ms to process per document. Testing on identical, heavily paraphrased, and unrelated documents revealed that the hybrid approach maintained an approximate detection capability of 68% for semantically rewritten texts compared to 6% for the TF-IDF baseline, while citation-aware filtering decreased the similarity score of an appropriately cited excerpt from 54.9% to 11.6%. SQLite and MySQL compatibility and light deployment requirements allow the system to operate on a standard server without requiring extensive optimisation.