Artificial intelligence (AI) has swept into the research landscape like an unforeseen gale, tossing ethical conventions into turbulence. This transformative technology has redefined traditional practices, creating unprecedented opportunities and challenges. This paper examines the ethical implications of AI assisted researchers attempting to publish in scientific journals. By examining the disruptions caused by AI, the paper highlights the need for re-imagined ethical frameworks to navigate this complex and evolving domain. Additionally, this study explores a proposed protocol and reference styling, focusing on integrating AI-related contributions in citations and methodology disclosures and verification protocols, to enhance accountability and reproducibility in AI-driven or AI-assisted research. This proposition aims to establish a standardized approach for recognizing AI’s role in the research process while upholding scientific ethics and integrity. It transforms AI from a silent assistant to an ethical partner.