The biggest difference between Earth's second atmosphere and its third (present) atmosphere is that oxygen from plant photosynthesis became a significant part of Earth's atmosphere.
The second atmosphere, primarily composed of gases released by volcanic activity (including carbon dioxide, water vapor, and other gases), did not contain free oxygen. The emergence of photosynthetic organisms, particularly cyanobacteria, introduced oxygen into the atmosphere, leading to the Great Oxygenation Event around 2.4 billion years ago. This dramatic increase in oxygen levels transformed the atmosphere, making it more conducive to the development of aerobic life forms and significantly changed the planet's environmental conditions.