User blog comment:AdmiralPedro1stFleet/Explaining the Origin of the Reapers (assuming the Catalyst is just Harbinger trying to indoctrinate Shepard)/@comment-68.145.117.128-20140602043934

Reapers are not synthetic life forms.

http://www.youtube.com/watch?v=y9hOwg62BL4&t=7m35s

Harbinger is the Catalyst:

http://www.youtube.com/watch?v=K-D4bBIzp4c&t=43m48s

Reaper motives aren't that complex.

Harbinger: We will bring your species into harmony with our own. (synthesis) Harbinger: We (Reapers) are your genetic destiny. Harbinger: You cannot escape your destiny Shepard.

Synthesis: Merge organic and Reaper DNA together to get husks or Reaper equivalent DNA. Saren: The relationship is symbiotic. Organic and machine intertwined. A union of flesh and steel. This is our destiny. Join Sovereign and experience a true rebirth. http://www.youtube.com/watch?v=2ICvVuYqP4A

Control: ASSUMING DIRECT CONTROL. Become an indoctrinated slave under Reaper control. As Vigil in ME1, and Vendetta/Javik in ME3 stated this is how they lost the war. Pick control, become indoctrinated.

The only option to defeat the Reapers and win the game is to destroy the Reapers. Much like the virtual world of the Geth Consensus, the ending looks familiar, and any changes made in the virtual world will affect things in the real world. Shooting the tube will fire the Crucible and destroy the Reapers in the real world. Reapers dead, Shepard wakes up. Shepard wins. He imagines his friends are safe (Extended Cut).

http://www.youtube.com/watch?v=Ws2gnrqBOLs&t=0m18s

Or simply put:

http://www.youtube.com/watch?v=p3h8ZnXLsRg&t=0m13s

The other choices are lies and tricks by Harbinger. An intelligent enemy like the Reapers will use trickery and deception in order to beat you. This is not bad writing at all. This is brilliant writing. How many game companies have been able to indoctrinate millions of people? Most people upset probably picked control/synthesis/refuse options. They, the players, were indoctrinated, not Shepard. Shepard is just a blank character you control and mould in your own image. Bioware indoctrinated you, to have the Reapers win. Or you realize something is off, pick the destroy option, and with enough EMS you kill the Reapers and win the game.