Neuropathy, kidney problems and elevated carbon-dyoxide

A 72-year-old patient was brought to the ER where they immediately transferred her to the Pulmonology department. She had very low oxygen saturation with high levels of carbon dioxide. She was intubated for 10 hours, and after that put on oxygen. Her condition improved for 6 days, but she started to express strange behavior, which was considered to be due to high CO2 levels. She was able to speak and walk, as well as to eat. However, on the 10th day after administration, she was unable to move, unresponsive to calls, only responsive to strong stimuli. On roentgenography, it was shown that she had some changes in her lungs, which was thought to be pneumonia in beginning. She was administered broad-spectrum antibiotics without isolating the pathogen. She is in unstable condition, unable to speak or respond, in an analgetic state. Along with her altered mental status, her kidney is not functioning well. In her history, there was no chronic illness, except hypertension which was put under control. She is a chronic smoker, has been smoking for almost 50 years. Three years ago she also had pneumonia and was in the hospital for 7 days. After that, she was sent home in a completely healthy state and doctors didn't find any abnormalities in her lungs.
My question is, if there is no harm to the lungs, except for pneumonia which she got inside the hospital, what is the reason for elevated CO2 levels, kidney problems, and peripheral neuropathy? Could it be that an infection lead to the formation of antibodies that are now attacking her nervous system and kidneys?