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

Why, if there was an easier-to-capture relay (as revealed in the Arrival DLC) and travel between relays is instantaneous didn't the reapers use that relay initially instead of announcing their presence and fighting the council's navy for the citadel relay?

Why, if possessing Saren meant his shield would die with him did Sovereign possess Saren (final boss transformation in ME1) instead of blasting Shepherd with his cannon?

Why, if possessing a sentient completely means the reaper's mind dies with it (as happened to Soverien) is Harbringer able to do so multiple times without consequence in ME2?

Why didn't Harbringer help Sovereign?

If Soveriegn was relied on to wake the other reapers from hibernation and he died why're they awake? Why was Harbringer awake?

Why, if Soveriegn could defeat the entire council navy alone, didn't he do so as soon as he found out the Protheans had tampered with the signal instead of working through proxies like the Rachni and Geth?

Why didn't Sovereign have an indoctrinated agent, like Saren, fix the Citadel signal so he could signal the reaper fleet?

If the travel time for the Reapers from their hibernation location to inhabited planets like Earth was less than a year (from the end of ME2 to the start of ME3) then why didn't they wake up and start traveling earlier, when Shepherd was dead?

If the Dr. in Arrival was indoctrinated why didn't she keep a low profile while the reapers came instead of getting caught, calling for help, and revealing her indoctrination to Shepherd?

Why, when the Reapers tried to kill Shepherd so many times in the past, would they spare him in Arrival?

What was the army of guards in the Arrival base doing that was more important than making sure Shepherd didn't escape captivity (there's two non-military personnel alone with Shepherd)?

If ME relays are nigh-indestructible, as evidenced by things like surviving a star going supernova, then why is an asteroid's impact enough to destroy one?

Why, if the Dr. was indoctrinated wouldn't she destroy the means (asteroid attraction) of destroying the relay?

How is a 3-man team not stealthy enough, especially given Shepherd's team could include a member like Thane, who's stealthier than him?

Why does Shepherd still take orders from the Alliance when by his death and working for Cerberus he's no longer a member of the Alliance?

How can any of TIM's actions in ME2 be explained if he was indoctrinated? Comics saying he was indoctrinated doesn't fill the hole in the game.