The Catalyst approaches Shepard and explains the purpose of the Reapers, as well as the ways in which Shepard can utilize the Crucible to stop them; Destruction, Control, or Synthesis. The availability of choices and the severity of the collateral damage on the galaxy will be determined entirely by the player's Effective Military Strength.
If EMS is between 0-1749, only the Destroy or Control option will be available (determined by whether or not the Collector Base was destroyed or preserved in Mass Effect 2). If the Collector Base was left intact, only the Control option is possible; if it was destroyed, only the Destroy ending will be available. Both options will result in massive physical damage to Earth, with Destroy killing everyone on Earth.
If EMS is between 1750-2349, the choice between Destroy or Control options becomes available, but either choice will cause some substantial damage to the galaxy.
If EMS is between 2350-2649, the Control option will cause no physical damage and the Destroy option will still massively damage the galaxy.
If EMS is 2650+ the Destroy and Control options will no longer cause any physical harm to the galaxy.
If EMS is 2800+ the Synthesis ending becomes available.
If EMS is 4000+ and the Destroy option is chosen, Shepard is seen barely alive, gasping for breath (if Anderson is shot by the Illusive Man, the player needs 5000+ EMS to see this short scene).[1][2]
The Destroy (red) option will result in the destruction of all synthetic life. The Crucible will fire a beam/pulse into the mass relay network, spreading the blast across the galaxy but destroying every relay in the process. The Citadel is also destroyed, breaking into pieces. Before choosing the Catalyst warns Shepard that it is possible new machines will be built in the future.
The Control (blue) option results in Shepard sacrificing corporeality to command the Reaper fleet. The Reapers will then leave Earth; presumably at the will of the Commander. Instead of firing a beam, only a pulse will be released from the Citadel. The pulse spreads throughout the mass relays network, causing them damage, but not as much as the other endings. No harm will be caused to the Citadel, which then seals itself.
In the Synthesis (green) ending, Shepard adds their energy to the Crucible's, thus creating a new, synthesized DNA. The Catalyst explains that this is the best option, since synthesis is the pinnacle of evolution, and will render the Reapers obsolete. The Crucible emits a green light/beam, altering all denizens of the galaxy on the genetic level. The mass relays are destroyed during the Crucible's use. The Citadel is also destroyed, breaking into pieces.
In every ending, the Crucible's blast causes the Normandy to crash land on an unknown planet. The survival of the Normandy's crew will rely solely on EMS:
If EMS is substantially low (below ~2000), nobody exits the Normandy.
If EMS is moderately high (above minimum, below maximum) and Destroy or Control are chosen, Joker and the player's most-favored crew mate will exit the ship.
If Synthesis is chosen, Joker, EDI, and the player's most-favored crew member will exit the ship. Joker and EDI will embrace.
If EMS is 4000+ then three crew members will exit in the Destroy and Control endings; Joker and two of the player's most-favored crew mates.[3][4]
After the credits, a scene will be shown in which an old Stargazer tells tales of "The Shepard" to a young child.