Neurodegenerative diseases and traumatic brain injury, whose hallmark features are the presence of focal axonal swellings (FAS), are leading causes of cognitive dysfunction. By leveraging biophysical observations of FAS statistics, we develop a theoretical model of functional neural network activity driven by adaptive changes from plasticity. Based upon the FORCE model of Sussillo and Abbott [1], our innovations highlight the role of plasticity in overcoming injuries and degeneration of neurons in a network architecture. We provide a quantitative measure, on a network level, of cognitive deficits arising from injury. We demonstrate that plasticity is capable of overcoming mild injuries while failing to compensate for more severe injuries. Such injuries are characterized by their underlying effect on spike trains propagating through the neurons in a network architecture. Specifically, spike trains can be filtered in firing rate, or blocked under more severe FAS. The level of injury dictates the FORCE model’s ability to produce a desired output functionality (and associated behavior) and allows for quantitative metrics for accessing cognitive and behavioral deficits. Thus a direct link between FAS in neural networks and compromised functional response can be established. The theoretical framework developed is a promising computational framework for providing a deeper understanding of the cognitive deficits arising in, for instance, Alzheimer’s, Parkinson’s, Multiple-Sclerosis, and TBI.