The ageing phenomenon of negative bias temperature instability (NBTI) continues to challenge the dynamic thermal management of modern FPGAs. Increased transistor density leads to thermal accumulation and propagates higher and non-uniform temperature variations across the FPGA. This aggravates the impact of NBTI on key PMOS transistor parameters such as threshold voltage and drain current. Where it ages the transistors, with a successive reduction in FPGA lifetime and reliability, it also challenges its security. The ingress of threshold voltage-triggered hardware Trojan, a stealthy and malicious electronic circuit, in the modern FPGA, is one such potential threat that could exploit NBTI and severely affect its performance. The development of an effective and efficient countermeasure against it is, therefore, highly critical. Accordingly, we present a comprehensive FPGA security scheme, comprising novel elements of hardware Trojan infection, detection, and mitigation, to protect FPGA applications against the hardware Trojan. Built around the threat model of a naval warship's integrated self-protection system (ISPS), we propose a threshold voltage-triggered hardware Trojan that operates in a threshold voltage region of 0.45V to 0.998V, consuming ultra-low power (10.5nW), and remaining stealthy with an area overhead as low as 1.5% for a 28 nm technology node. The hardware Trojan detection sub-scheme provides a unique lightweight threshold voltage-aware sensor with a detection sensitivity of 0.251mV/nA. With fixed and dynamic ring oscillatorbased sensor segments, the precise measurement of frequency and delay variations in response to shifts in the threshold voltage of a PMOS transistor is also proposed. Finally, the FPGA security scheme is reinforced with an online transistor dynamic scaling (OTDS) to mitigate the impact of hardware Trojan through run-time tolerant circuitry capable of identifying critical gates with worst-case drain current degradation. INDEX TERMS Ageing mechanism, field programmable gate array (FPGA), hardware Trojan, negative bias temperature instability (NBTI), propagation delay, reliability, threshold voltage. I. INTRODUCTION A modern FPGA is not merely an emulator but a hardware accelerator with heterogenous hard IP cores, such as complex memory blocks, multiple processors, and DSP blocks. Systems on chip (SoC), network on chip (NoC), and adaptive compute acceleration platform (ACAP) are the significant performance and functional enhancements of FPGAs, that have been made possible due to the continual shrinking of transistor sizes down to the scales of 10 nm and below. The performance benefits, however, are limited by power The associate editor coordinating the review of this manuscript and approving it for publication was Luis Javier Garcia Villalba. and timing closures. Similarly, the geometric structures of FPGAs with much less silicon and relatively more oxide and moulding compound complicate the heat conduction paths [1]. On the one hand, where it may deteriorate the worstcase heat dissi...