The Manhattan Project: Second Stage consists of four small expansions that can be added to the base game individually or together.

- Nations 2 works like the previous Nations expansion, with each player getting one card to represent a country and gain a special power. Seven new countries and powers are represented.

- Rocket Technology allows you to build a rocket factory when taking the "Design Bomb" action. Rockets work exactly like bombers - but fighters provide no defense against them.

- H-Bomb Technology upgrades the "Design Bomb" action, allowing a player to return an available bomb to the bottom of the deck in order to acquire an H-Bomb card. To build an H-Bomb, however, the player needs Lithium Deuteride, which comes from new cards that work similar to Mines.

- Personalities adds seven roles to the game based on real individuals who contributed to the Manhattan Project. Each time you retrieve your workers you will select a different role. Each role will grant you persistent benefits until the next time you retrieve.