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ME1 | 1. Why weren't there geth ships to guard both ends of the Mu Relay (to counter the Normandy's stealth), and how did Joker fly out once they were alerted to their presence?[/quote]Presumably, most of the geth fleet was getting ready to launch the surprise attack on the Citadel. Saren also didn't really have any reason to believe that a newbie Spectre, and a
human no less, was so close on his tail. Geth ships could have pursuded Joker after the fact, since we don't hear anything from him after touch down on Ilos
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ME2 | 2. Why didn't the Collectors try to abduct the Normandy SR-1 crew instead of destroy them?[/quote]Presumably with Shepard and the Reaper Busters on board, it was considered far too risky to attempt to board than it was to simply blow them out of orbit. The Normandy doesn't really have a large crew so it wouldn't make a significant dent in their plans even if they did manage to abduct all of them. They may come out as a loss too, considering they'd probably lose some Scions and a Praetorian in the process.
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ME1 | 3. Couldn't the Turian Councilor accuse Shepard and Tali of pre-recording Saren's voiceprint during the "trial" and modifying it to say what they want (like in Kasumi's DLC)?[/quote]Given that on of Aria's bodyguard has a magic tool that can detect whether or not you're the original Shepard and not just a bio-engineered impostor with a 2-second scan, the Council probably has access to the technology to determine whether or not the data from the geth's memory core had been tampered with, and whether or not the voices were legitimate.
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ME2 | 4. How DID Shepard's body remain intact during the descent into Alchera or his orbit around it?[/quote]It's implied that Shep didn't, really. "Nothing more than meat and tubes" was what I believe the words used were. Also, if memory serves, Alchera didn't have much of an atmosphere, which would alleviate the re-entry fires, assuming they weren't just in low orbit (which would imply very little decay if someone grabbed the body within hours). If the body actually did hit the ground, those hardsuits better have been pretty awesome to contain the splatter.
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ME1 | 5. If recording was that simple, why didn't they use it during their conversations with Saren, Sovereign and Vigil? After all, a solier from Ashley's team was able
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dmet recordings of Sovereign in the middle of battle (why didn't they use that too?)[/quote]Got nothing on this one, really. Unless Shep just didn't have them.
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ME2 | 6. Why are there dog tags in intact crates on Alchera? Did crew members think that hiding in crates would help them survive?[/quote]I assumed that they were underneath the crates, basically trying to affect a simple idea of "searching through rubble"
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ME1 | 7. In Bring Down the Sky, why didn't Balak just set the bomb charges off while Shepard was disabling it to kill two birds with one stone?[/quote]Then there would have been nothing stopping the Normandy from blowing him out of the sky. Granted, there wasn't a lot to stop the Normandy from tailing him in stealth mode and then doing it anyway, but that's a plot grievance for another time.
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ME2 | 8. Why wasn't Shepard and Jacob more suspicious of the fact that Wilson was in a room by himself with human corpses and a wounded leg?[/quote]Because there was an army of robots rampaging all over the facility, shooting people. Bigger concerns at the moement. Also why a majority of
players didn't notice it on their first playthrough.
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ME1 | 9. Why wasn't Shepard suspicious enough to ask Ian Newstead how he managed to get past all the geth in the Feros tunnels? Is the Thorian allied with the geth or something?[/quote]The geth were fighting the Thorian thralls, since he was still actively resisting the effect of the spores, it's possible that he had simply been down there for a while and unnoticed. It is a bit of a hole that you can't ask him about that though.
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ME2 | 10. If Garrus wasn't recruited in ME1, why does he still act like he's known Shepard personally through all the "old times"?[/quote]It's pretty hard not to recruit Garrus in the first one. You could chalk it up to him ribbing Shepard about being the glaxy-slaying geth-killing powerhouse that he's probably currently known to be. I would be surprised if Garrus/Wrex being optional wasn't actually intended in the first place.
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ME1 | 11. If you let Fist live, why didn't the Shadow Broker hire anyone to go after Fist again, or to go after Wrex for betraying him like Fist did?[/quote]Bigger concerns, Fist is still ruined, his bar's been shot to pieces and his betrayal is easily keeping him out of anythign meaningful in the information brokering business.
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ME2 | 12. Why didn't Warden Kuril in Purgatory wait until Shepard and squad stepped INSIDE the cell before closing it on them?[/quote]Shep and Co already refused to drop their weapons and get in the cell, and closing it once battle begins prevents the plot hole of "why doesn't the sell lock me in when I step in?"
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ME1 | 13. Why couldn't the geth or Saren just attach explosives to all the elevators in Feros, Noveria, Virmire, Ilos and the Citadel to get rid of Shepard?[/quote]That's... really reaching.
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ME2 | 14. If Garrus knew how to take down a gunship in one shot, why didn't he do that the second time instead of shooting at all the offloaded mercs?[/quote]I may have missed something in the dialog, but as far as I can tell, there's nothing to say that he did. Even if he did damage it enough to disengage, that would have to be a really lucky shot.
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ME1 | 15. If the Mako's jets only work for a few seconds, how does it get back to the Normandy without forcing the Normandy to land?[/quote]Either the Normandy does actually land, or a specialized shuttle can load and offload the Mako. The idea of a loader/offloader is supported by the Mako conveniently appearing in the garages you go to.
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ME2 | 16. If Haestrom's sun destroys all shields and Quarian technology - including Legion (but not Grunt's armor) - why are the other geth unaffected?[/quote]Gameplay and story segregation. It would be quite a task to make sure that the Geth's AI avoids arbitrary spots where good cover or manueverable ground exists. Alternatively, since Haestrom is in Heretic space, the Heretics have specialized shield generators to deal with it.
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ME1 | 17. If the Mako can't fire upwards and has limited mobility, why didn't combat drones just hover over the Mako and fire at it from above?[/quote]The Mako can fire upwards, simply at a limited angle, much like most modern tanks and APCs. Also, the Mako is highly mobile and could just reposition itself at an angle where it could hit the drones again, or Shep and Co could simply engage it on foot. The drones also seem to have a relatively low maximim altitude, the aren't fighter planes.
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ME2 | 18. If Haestrom's radiation prevents all off-world communication, how does EDI immediately contact Shepard after?[/quote]Got nothing. Maybe Shep just has better tech. Quarians aren't exactly rich, doesn't explain the Geth though.
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ME1 | 19. Why didn't Saren destroy the second beacon on Virmire after using it to prevent Shepard from doing the same?[/quote]Because it was in the dead center of his impenetrable doom fortress. Not to mention it's a reather handy resource to keep around.
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ME2 | 20. Why does Maelon mention "Reaper indoctrination" specifically when referring to Mordin's past research when no one knew about it before then?[/quote]The Salarian STG was aware of it by at least the events of ME1. Since Mordin was still in high standing, he could have easily been taken in as a consult on this.
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ME1 | 21. If Shepard chose to go to the AA Tower, why didn't Saren and the geth just eliminate whoever stayed back at the bomb site and either disable or take the bomb out of the facility?[/quote]By attacking the bomb site, that was
exactly what they were trying to do. Ashley (or whoever you killed) armed the bomb so that "this thing goes off no matter what."
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ME2 | 22. If the Disabled Collector Vessel was a trap by the Collectors, why would they leave behind a large cache of upgraded weapons for Shepard to pick from?[/quote]Gameplay and story segregation again. It's shown that you have plenty of guns already on the Normandy, that was probably just the pile of random weaponry they picked up during their raids. Given that it was next to the dead collector, it's entirely possible that they were running tests on human weaponry as well.
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ME1 | 23. Opold in Noveria asks you to smuggle weaponry because they check everyone's belongings and shipments for weapons - except Spectres. How was Matriarch Benezia able to carry all that cargo with her when the weapons can be detected (even though the inactive geth can't)?[/quote]Bribes. Benezia represents Saren, one of the biggest investors on both Noveria and for whatever company it was out there, can't remember at the moment. Alternatively, Geth weapons can be hidden in the same way that the Geth can.
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ME2 | 24. How did they know the Derelict Reaper was 37 million years old, if the Council was incapable of testing any of Sovereign's parts?[/quote]Cerberus was the group who found the derelict Reaper. I had assumed that the 37 million came from the time that it had been laying there "dead" anyway. Saying it's a 37 million year-old wreck instead of the wreck of 37 million yeard old ship.
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ME1 | 25. If you go to Virmire with Wrex but haven't recruited Garrus or Liara yet, Wrex will automatically agree with you to destroy the genophage regardless of what you say to him. Why?[/quote]Got nothing.
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ME2 | 26. Mordin told Shepard that they made covert drops of the modified genophage on Tuchanka's water supplies and hospitals. What about all the krogan in the rest of the galaxy?[/quote]The Krogan throughout the rest of the galaxy aren't breeding, they're going off to fight and die. Considering that the Krogan don't have any colony worlds anymore either, the overwhelming majority of the populaiton is on Tuchanka, and the Krogan elsewhere will make little to no difference (also, the Genophage will probably have to be modified again anyway).
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ME1 | 27. On Therum, if there were so many enemies (including underground), why didn't any of them use the mining laser first to get around the barrier?[/quote]They couldn't figure out how it worked or realized that cutting into the incredibly unstable rock around an active volcano was a monstorously stupid plan.
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ME2 | 28. Why are there mechs and heat sinks in Aeia when Ronald Taylor and crew were stranded there 10 years ago? (commonly asked question)[/quote]Gameplay and story segregation. This thermal clips are a legitimate plot hole, but security mechs were adopted into
wide usage after the Battle of the Citadel, so it's not impossible for a ship to have them, especially if they're trying to set up a colony.
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ME1 | 29. Why did the Thorian attach itself above a seemingly bottomless pit to fall down in?[/quote]Looks forboding.
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ME2 | 30. The Illusive Man said that an Alliance science team discovered the great rift on Klendagon, but it was a Cerberus team that traced the location of the Derelict Reaper. What happened to the Alliance science team?[/quote]Take your pick: (a) They didn't track it to the Derelict Reaper (

Cerberus bought them © Cerberus killed them. It's not mentioned because it's not a need to know detail.
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ME1 | 31. If either Ashley or Kaidan are left behind by themselves in the Virmire multi-squad mission and two other squadmates are with Shepard, what are the other two doing?[/quote]Same thing that your whole squad does when on any other planet. Twiddling their thumbs. This is a definite gaping plot hole.
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ME2 | 32. Was Legion saying that Shepard talked to Sovereign on Ilos writer oversight or did the geth really make a mistake?[/quote]Oversight.
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ME1 | 33. If hanar are allowed to roam on the Presidium, where is their Embassy and where is the Hanar Ambassador?[/quote]Places you haven't been to yet.
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ME2 | 34. Why didn't the crew test the Reaper IFF near the Citadel fleet? Was there supposed to be some kind of actual multi-squad mission they needed to do?[/quote]It's a Cerberus vessel, Cerberus tries to avoid main government interference (especially them dirty aliens). Wihout knowing that happens beforehand, there's no reason not to try it away from an assisting fleet. Miranda also mentions that "you can pick who you want to go with when we get there" that is, when you get the full intel about the mission. This bit is only a plot hole if you have no more missions or assignments to do. Otherwise, presumable you were on route to do one of them before hearing that the Normandy was under attack.
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ME1 | 35. Why didn't the Normandy SR-1 just use its Reaper-slaying cannons instead of the Mako in the Ilos ruins the moment they saw Saren walk in?[/quote]About a million different reasons. No idea what it would do to the structure, no idea on whether or not it would block Saren, starships probably have difficulty dealing with targets they're not designed to deal with (like Infantry), could just as easily block your progress as it could kill Saren.
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ME2 | 36. After the Mass Effect core was destroyed in the Derelict Reaper and they floated over to the Normandy (suggesting the Reaper no longer has its own gravity), why didn't they immediately start falling into Mnemosyne instead?[/quote]Still in orbit, low weight.
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ME1 | 37. Why did the Protheans disable the Keepers' reaction to open the Citadel relay instead of disabling the relay portion of the Citadel itself (both the Keepers and the Citadel are advanced technology, after all)?[/quote]Knowing how to do one and not the other. The game mentions that the Protheans were just beginning to understand how the Mass Relays work, there's also no guarantee that the keepers wouldn't do, you know, exactly what they were programmed to do and repair it.
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ME2 | 38. Why did the Collector Base only have one ship to defend itself when the Base itself is the size of a planet?[/quote]The base isn't the size of the planet, and there aren't all that many Collectors.
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ME1 | 39. If Turian husks (Saren) have more reach and flexibility than human husks, why didn't Sovereign just convert all the Turians he found?[/quote]Saren wasn't a husk. Definitely not a traditional one at any rate. He was implanted by Sovereign instead of the normal husking process, and only got those boss moves after all of his flesh was burned away in an appropriately dramatic cutscene.
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ME2 | 40. Why does Grunt die as Second Fire Team Leader because his shields went down (he has armor, not shields)?[/quote]When is it mentioned that he only has armor? It's perfectly possible to have both.
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ME1 | 41. How does the Citadel Rapid Transit shuttle manage to get into enclosed spaces like the hallway in Chora's Den?[/quote]I think you need to look up what a "plot hole" actually is. Probably just a design oversight.
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ME2 | 42. Why didn't the diversion team (the one without the biotic barrier) get attacked by massive amounts of seeker swarms?[/quote]Not part of their defense plan, it's generally implied that the Collectors never expexted to have to fight on their own turf, or you were keeping the seekers busy.
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ME1 | 43. If Shepard eliminates the Council and replaces it with a new, all-human Council, why can't Udina and Anderson both be on it?[/quote]Udina's a dick and doesn't care for Anderson. Anderson doesn't have much of an actual interest in politics and red tape.
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ME2 | 44. Why were we forced into joining Cerberus? I wanted to side with the Shadow Broker.[/quote]The Shadow Broker tried to sell your corpse to the Collectors, that wouldn't have gone over well. Not to mention the difficulties in getting ahold of the Shadow Broker to begin with.
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ME1 | 45. Why were we forced into joining the Council Spectres? I wanted to side with Saren.[/quote]You're really reaching. This isn't even a plot hole.
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ME2 | 46. Why are Tali and Garrus (and all the aliens on the ship) more trusting of Shepard working with Cerberus than Ashley and Kaidan?[/quote]Mordin joins out of personal interest, the rest of the Aliens are joining through you without being told up-front that this is indeed a Cerberus Operation. Meanwhile, since Cerberus is a rogue group, it's natural that the big Alliance patriot is going to be a whole lot less understanding than the people you've recruited and convinced personally. Tali also remains pretty grumbly about the whole thing.