In a nutshell: old age.
Today, a leaked photo of Stan Lee's death certificate has confirmed his cause of death. As we so often do, with celebrity deaths, the specifics of Stan Lee's death have come leaked and much later than the the day he died. Thankfully, though, Lee's death seems a peaceful one. Unlike so many recent celebrity deaths where there's fentanyl involved (Mac Miller, Prince, Demi Lovato, who actually survived), Lee's passing is about as close as you can get to 'natural causes.'
The document, which you can view here, cites Cardiac Arrest as the "immediate cause," with respiratory failure and congestive heart failure entered as the "underlying cause," meaning a "disease or injury that initiated the events resulting in death." These causes are all strictly in-the-moment though. The over-arching sickness that Lee had been having an on-and-off battle with was "aspiration pneumonia" which is, according to Healthline, "a complication of pulmonary aspiration. Pulmonary aspiration is when you inhale food, stomach acid, or saliva into your lungs. You can also aspirate food that travels back up from your stomach to your esophagus." When they go into the lungs, "these things may carry bacteria that affect your lungs." If you have healthy lungs it's not a big problem, but if they're older and more brittle, "pneumonia can develop as a complication."
Lee was 95 when he died on November 12th.