User blog comment:Suparockr/List of Plotholes throughout the series/@comment-68.98.139.63-20120720205039/@comment-1221773-20120720212154

None of those are plot holes. Frankly, I'm beginning to wonder if people are actually paying attention when they play the games.

1. Using the Citadel relay is faster and allows the Reapers to decapitate the galactic government and take control of the mass relay network.

2. The arrogance of villains. Sovereign thought he could beat Shepard. It's also possible that Sovereign was unaware that he would be incapacitated if he lost; by the time the Reapers arrive at the galaxy, it is noted they corrected this design flaw, which implies that up until Sovereign's defeat they were wholly unaware of the flaw too.

3. Sovereign didn't die when Shepard destroyed the Saren avatar, it was just incapacitated.

4. Harbinger was hibernating with the other Reapers in dark space. Sovereign was supposed to be alone so he could observe the galaxy and activate the Citadel relay at the most opportune time without the existence of the Reapers being revealed beforehand.

5. Sovereign probably woke the other Reapers up so they could enter the galaxy through the Citadel relay once he activated. The Reapers don't appear to have any limits on communicating with each other, Harbinger could control the Collector General in real time from half a galaxy away.

6. There's no conclusive evidence Sovereign ever used the rachni or was even active before Saren discovered him. As for the geth, he needed their help and Saren's to locate the Conduit so Saren could get inside the Citadel and disable its security systems in order for Sovereign to interface with the Citadel undisturbed.

7. The signal wasn't altered, the Protheans altered the keepers' ability to perceive that signal (and the signal's purpose was to have the keepers activate the Citadel relay). It's unlikely Saren could have figured out how to change the keepers back given how little modern races know about them.

8. The Reapers began traveling to the galaxy as soon as Sovereign failed. That's around two and a half years of travel time to the Alpha Relay, with six months added because the Alpha Relay was destroyed.

9. Dr. Kenson was captured the batarians unexpectedly, she did not send for help (Hackett hadn't heard from her in a while, thought something was amiss, and called in Shepard to investigate), and she probably thought Shepard would be indoctrinated as well or captured (and Shepard was captured and knocked out for days. If Shepard had been knocked out for two more hours, the Reapers would have arrived).

10. The Reapers never had the chance to directly kill Shepard in Arrival. As I noted above, that Shepard woke up (I believe the scientists were either experimenting on him or holding him for the Reapers) before the Reapers arrived was pretty much a fluke.

11. Again, they probably didn't think Shepard would wake up. Play Arrival again and listen to the scientists speaking as Shepard woke up.

12. Play Arrival again and listen to Kensn explain why an asteroid impact can destroy a mass relay. Mass relays were only assumed to be indestructible, no one ever tried before.

13. The asteroid contained Object Rho, a beacon that the Reapers were using to navigate to the galaxy. Play Arrival again.

14. As simple as game-logic. The devs wanted to give Shepard a solo mission.

15. The Arrival mission was a favor to Hackett, and Shepard still has some loyalty to the Alliance.

16. The Illusive Man wasn't completely indoctrinated until he fled to the Citadel and joined the Reapers. Up until then, he was working to control the Reapers for the benefit of humanity.