So, this has been brought up countless times but I'd like to reiterate myself just to create a more clear definition of how the story could continue.
Basically, everything from the point after Harbinger attempts to kill you is an illusion. There is enough in-game proof to support this theory. All of it is a hallucination created by Harbinger's final push to indoctrinate Shepard.
When we see Anderson and TIM at the console, it is the psychological manifestations of Shepard's Paragon and Renegade sides. The fact that Shepard is unable to have any real interaction during the majority of the exchange, forcing Shepard to witness the conflict. Even TIM attempts to force Shepard to kill Anderson, who is the vision of Shepard's resolve.
When talking to Catalyst, it becomes very obvious that it is not just simple a neutral controller for the Reapers, but serves the same purpose as the Reapers. It purposely paints the Destroy option as a bad idea and appeals to Shepard's armor and humanity to try and convince the Commander to pick both either Control or Synthesis. Even the colors on Destroy and Control are completely opposite of their true nature, considernig Anderson is shown on the Destroy side and TIM is shown on the Control side.
The three decisions boil down to these basic concepts
Destroy: Shepard resists Harbinger's final attempt at indoctrinating him/her
Control: Shepard wililngly gives into the indoctrination
Synthesis: Shepard is tricked into believing that this will finally bring peace and inadvertantly succumbs to indoctrination just like Saren did in ME1
The EMS score's role in this determines not only Shepard's available options, Catalyst's responses, or the outcome, but also the possible impact Shepard's hallucinated choice will have in the finale. Low EMS likely results in failure no matter which decision you chose. Your forces will be overwhelmed and destroyed by the Reapers and the cycle will continue.
However, with high EMS, these could be possible variants to the outcome.
Destroy: Shepard awakens and finds themselves buried under rubble, but alive. Harbinger is still twarting all attempts to reach the Conduit. With Shepard still alive, the resistence keeps fighting and make it to the Conduit and onto the Citadel to activate the Crucible and destroy the Reapers once and for all
Control: Shepard's very being and conciousness is absorbed by Catalyst and becomes a part of the Reaper control VI program, turning Shepard into a sleeper agent for the Reapers. He/she either awakens or dead body is found and taken by Reaper troops to be repurposed to being their next Vanguard.
Synthesis: Shepard's DNA and conciousness becomes apart of the Reapers, giving them a better understanding of humanity's tenacious will power. Either Shepard dies or becomes one of the Reapers themselves, carrying out the destruction of his own people and allies. That or you get the same sleeper agent ending as Control.
The ending possiblities are just my ideas of what could happen given the circumstances. Given that the titles for each option speak for themselves about the possible outcomes of the choices, it's wouldn't be too far off.