Having just about finished this up this evening I came to the realisation that this game is about one woman's decent into madness.
Think about it.
Jonah escapes multiple situations far worse than Lara faces and shows up with no real explanation with no sign of harm. On more than one occasion he is able to walk towards floods or explosions only to be fine moments later. He also seems to show up just before terrible and sometimes apocalyptic scale situations happen. The paracite at the beginning is a representation of Lara's sanity. By removing it she has acknowledged on a subconscious level she has no further grip on reality.
Lara meanwhile believes she has caused multiple catastrophic incedents resulting in the loss of hundreds if not thousands of lives. That alone is enough for someone to demonstrate a very lose grip on reality. But the fact she shows little actual remorse for the massive loss of life she believes she has caused shows how deeply disturbed she is. Her only response is to murder hundreds of trinity workers in increasingly brutal ways. Encouraged by her faithful assistant Jonah...