The last, but the most important choice of the Mass Effect Trilogy. You’ll have to choose between four options on what to do with the Crucible.
Choice: Control, Destroy, Refuse, and Synthesis
The final choice in Mass Effect 3 is determined by your Effective Military Strength (EMS), and the availability of the choices available depends on how high it was when you get to this point.
By choosing Control, the Crucible will absorb your soul, then upload it to the Reapers. If your EMS is below 2,649, this act will destroy all the Mass Relays, and ravage Earth. Furthermore, your narration will change, depending on your morality score, this will be one of three outcomes, Paragon, Renegade, or Neutral.
By choosing Destroy, the Reapers will become disabled, and inoperable due to the Crucible’s energy waves. If you choose this choice whilst you’re at 3,099 or higher, you could live through this, but only if Anderson survives the Illusive Man, and if you’re above 3,100 EMS, you’re guaranteed to survive. At 2,649 EMS or lower, you’ll destroy all the Mass Relays, and ravage Earth. If your EMS is lower than 1,749, you’ll kill all life on Earth. Regardless of your EMS score, you’ll end up killing all non-organic life in the galaxy, including EDI, and the Geth.
By choosing Refuse, by choosing “I reject these options”. You’ll get a speech option, and this’ll let the Reapers continue with their extinction plan, which won’t get stopped until the next cycle, in 50,000 years. You can also shoot the catalyst, which will result in the same outcome minus the speech.
This choice is only available at 2,800 EMS or higher, and will transfer your soul into the crucible, then used in an energy wave, which’ll change all life into organic and in-organic beings, thus giving the Reapers no reason to make you extinct anymore as they consider you allies.