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Mass Effect 2
The quarians must stay in environmentally-sealed suits at all times, even while on-board their starships, to ensure they don't get sick. Outsiders also must wear environmental suits while on quarian ships to ensure they don't spread disease. Which doesn't explain why Miranda is walking around in her normal Stripperific outfit with the addition of a mouth-nose mask.
Hell, every single squadmate has this problem; not just on the Migrant Fleet, but in dozens of places where they shouldn't be able to survive. Particularly egregious, since in the first game everyone had sealed environmental suits. It's little wonder why users on the Bioware forums have yelled loudly after the game was released for all the characters to get, at the very least, a suit of armor. Poor Jack goes through most of the game wearing nothing but some pants and a few strategically-placed strips of material to cover herself. The only cosmetic change she gets after unlocking her loyalty is a shirt, if that because that alternate costume looks more like she got one sloppily added near full torso tattoo.
Zaeed's loyalty mission: Save the refinery workers or go after Vido? Why do we have to choose? Saving the workers wasn't hard! Why couldn't we just have squad member #2 take care of the fire extinguishers while Zaeed and Shepard track down Vido? It's not like it'd be the only time Shepard did a mission without two buddies to back him/her up! The third game addressed this silliness by having moments where squadmates can go off to do tasks by themselves during certain missions.
The infamous moment where Shepard encounters Ashley/Kaidan on Horizon. When your former squadmate gives you the What the Hell, Hero? speech about joining up with a group of monsters like Cerberus, Shepard's best response s/he can give is something along the lines of "Cerebus isn't your enemy this time." Why can't you have him/her say that they don't trust Cerberus at all, are only reluctantly working with them because of their mutual enemy in the Collectors, is about as happy about it as s/he was about the Council screwing them over and barring them from going to Ilos, and if the Illusive Man tries any bullshit they're going to hightail it out of there and work solo? It wouldn't so bad if it wasn't for the fact that Shepard does get to say things along these lines repeatedly both before and after this event! Then why, during their encounter with someone who should be at least one of their closet friends, does s/he decide to not say anything like this?!
The ending decision of the game. You can either choose to destroy the Collector Base or hand it over to Cerberus for study. Why can't you choose to hand it over to the Alliance or the Council? Or if you choose to destroy it, you do so on the basis of the many atrocities committed at the Collector Base. Why can't you point out that it involves Reaper tech and would likely Indoctrinate any Cerberus personnel sent to work there?
Mass Effect 3
The third game has so many off-kilter and headscratching moments that some players have accused Bioware of outright sabotaging the franchise and/or rushing the game to meet a release date instead of fixing the narrative. This document is the tip of the iceberg when it comes to stupid plot decisions, and further elaborated upon in thesethreevideos. The ending particularly enraged fans, mostly due to it being poorly written and fitting in poorly with the rest of the game, and the rest of the series, and taking away player agency.
Shepard's behaviour during the prologue and Defense Committee meeting is bizarrely inconsistent. S/he starts off by telling the committee that it isn't the time to fight, only survive. Seconds later, s/he tells the committee that humanity has to fight or die, completely ignoring that (depending on your playthrough) Shepard has already overcome the odds multiple times by rallying various factions/specialists and accomplishing missions that were previously thought impossible. Later on, when Shepard gets on the Normandy, Anderson has to expressly tell him/her to rally the galaxy, even though Shepard is insistent that the fight is on Earth. Was Shepard dumbed-down deliberately or accidentally?
Despite the fact that the Reapers took over the Citadel (offscreen, rendering the time you spent building that "Citadel Defense Force" completely pointless) and shut down the Mass Relay network, they somehow failed (or outright forgot) to shut down the Charon Relay, giving the Alliance forces and amassed fleets the perfect opportunity to get into the Sol System. Furthermore, they wait until TIM gives them the warning about the Crucible to attack the Citadel, which would allow them to control all the other Mass Relays. As opposed to, you know, attacking it immediately so the other species can't unite against them. Even worse, why did the Reapers move the Citadel to Earth (a planet that still has a large resistance force fighting) when it could be moved to a more controlled territory like Thessia, which was completely taken over at that point? And why did the Reapers keep the damn Conduit on? If they had turned it off (or better yet if they had just taken control of Citadel and closed it from the inside and left it where it was), it would be impossible for anyone to penetrate it, thus the Crucible would be useless, and resistance to the Reapers would (probably) be crushed.
The treatment of several of the ME2 squadmates, and their reasons for not joining Shepard on the Normandy (and becoming an assistant/teammate), are downright absurd. This is very strange, considering that the narrative goes to great lengths to show that many of the squad members (including James, Garrus, Tali and EDI are handling important tasks or work on their own when they're not on a mission with Shepard. While some have good reasons for staying out of the fight (Jack has to protect her students, Grunt is leading Aralakh Company, Thane is too sick), others have no excuse.
Miranda has to sneak around all the time to avoid Cerberus forces, but rejects your offer to come aboard (and give her resources) with the statement that this is something she has to do herself. She was second-in-command of the Normandy, one of the highest placed members of Cerberus, and yet she could fulfill the same role onboard the Normandy (or lead anti-Cerberus efforts)! Instead, she spends the majority of the game hiding and looking for her sister. On the off-chance that Miranda died in the last game, Oriana sends you an e-mail anyway about what's happening on Sanctuary, making the former's role completely pointless.
Samara pledges once again to fight for you no matter what happens...and spends the rest of the game standing around in the Citadel doing nothing. Zaeed (if he survived) is genuinely happy to see you, but sits around in the Citadel refugee ward for the rest of the game talking about how he'll help you take Earth later.
The EMS system, according to some reviews and players, is a confusing, jumbled mess that assigns arbitrary point values to every ship, crew member and asset without thoroughly explaining how any of them relate to each other. This can cause headscratching moments when certain assets are compared with each other, such as:
Diana Allers, a journalist who is serving onboard the Alliance flagship and is providing Earth with exclusive interviews and updates about the status of the war, is worth 5 points. Khalisah Al-Jilani, a tabloid reporter who has one conversation with Shepard in the game, is worth twice that much, despite not having the same access as Allers.
Throughout the game, Shepard can amass War Assets for a "Citadel Defense Force", which (if the in-game descriptions are any indication) are providing supplies and assistance to residents across the station. Come the endgame, the Citadel is commandeered by the Reapers, and the fate of its inhabitants is never addressed again. While rumors suggest that there were plans to have the CDF matter in the endgame (its value would determine whether or not the occupants escaped in time), they have no current purpose in the game, and there is no reason to obtain assets for it beyond artificially inflating the EMS score.
The net result of letting Captain Kirrahe die on Virmire (which nets an exclusive asset, the Salarian Special Tasks Group, worth 35 points) is worth more than keeping him alive, despite it taking more effort in ME1 to ensure his survival.
During the Cerberus Coup mission, if you haven't convinced the Virmire Survivor that you're no longer working with Cerberus, they'll turn on you and protect Udina while he attempts to open the door for the Cerberus troops to come through. This leads to Shepard or his/her squadmate shooting Ashley/Kaidan in the stomach. The wall banger is that, despite the fact that A/K are wearing full armor, their shields and health magically fail at the right moment and they're downed by a single bullet, whereas they can soak up bullets, lasers and more in normal gameplay. No one bothers to help or use Medigel on them.
The endings. So many illogical and downright bizarre moments occur in the last ten minutes that the narrative collapses under the weight of a boatload of silliness:
To start is one of the key reasons as to why this was so reviled: it was pulled as a Shocking Swerve. There was no foreshadowing, not even a subtle hint that the Crucible was created millenia ago, nor that it had an on-board VI/AI. Compare that to Dragon Age: Origins, which spelled it out a full hour before you'd reach the ending that "One of the Grey Wardens will need to die to defeat the Blight", and the upset is understandable - BioWare had done such things before, but had given time for the players to cope/decide before hitting them with it.
The Crucible. Throughout the entire game, you've been amassing scientists, technicians and special teams of various species to work on this unknown device, whose apparent purpose is to dock with the Citadel and do...something. None of the main characters have any idea what this device does, yet they rely on it as a Hail Mary pass to defeat the Reapers. No one told Shepard how to activate this thing when he finally got to the control panel to activate it? And better yet, why did a continuous cycle of species, over billions of years, add pieces to it without having any idea what it was capable of?
The main motive of the Catalyst boils down to "organics shouldn't be killed by synthetics, so I made machine gods that will harvest you every 50,000 years...to save you from synthetics." Why did Shepard not question how stupid and redundant that was? S/he just rolls over and accepts it.
The Catalyst (and the plot, by extension) ignores the fact that in spite of its claim that organics and synthetics cannot co-exist, Shepard has spent the entire game possibly rallying both types of life. One instance always occurs (Joker and EDI begin a relationship), while it is possible to broker peace between the Geth and Quarians. Yet, Shepard never bothers to bring this up or throw the Catalyst's claim back in its face, making him/her look like a fool.
Made worse considering the Geth are among the kindest race you meet in the entire series. Legion (who is part of the hive mind so he's capable of speaking for his whole race, Heritics aside) is constantly helpful and kind to you and your cause, only coming into conflict if something life or death gets in the way such as the Quarians trying to wipe them out. You even learn that the single thing the Geth truly wanted was to live in peace with their creators who won't stop trying to shoot them in the face. It's really hard to stomach that you're supposed to just believe the race of robots with the attitudes of loyal butlers is some how more prone to going insane and evil than any of the other races whom are much more trigger happy. Hell, then you learn of the Protheans who established a galactic empire, for some reason them being organic and ruling the galaxy is better than if they were robots and still ruled the galaxy.
The game ends with (depending on your playthrough) the squadmates you took with you on the final mission somehow teleporting back to the Normandy and crashlanding on an unknown planet. This occurs even if your EMS is low enough that they died on the way to the Conduit (with their bodies lying on the ground as you walk towards it after Harbinger's attack).
The Extended Cut resolves the question of what happened to the player's squadmates, via a new scene that shows the Normandy landing to evacuate them and offload more assault troops. However, this raises another moment of stupidity. Harbinger (who, up to this point, has been targeting and destroying ground units and vehicles) apparently does nothing while the ship that destroyed the Collector Base lands right in front of it and Shepard puts his/her team onboard. Even worse is that the way the scene is presented; the ship lifts up and takes off while Harbinger just sits there and watches it without firing or doing anything. Even worse, the added scene requires Joker to break off from the dogfight he is quite busy with when Shepard contacts him, travel through an atmosphere (where the Normandy can't move at anything resembling light-speed for obvious reasons), and arrive at Shepard's position in about 5 seconds (which is literally how long the Normandy takes before it arrives on-screen).
Immediately following Shepard's choice, Joker is seen flying the Normandy through the Charon relay and attempting to outrun the massive blast wave behind him (to the point that he looks backwards on the ship when there's nothing to see but the CIC behind his cockpit). Let's reiterate: the guy who provided fire support for Shepard and the two teammates s/he took with him/her on the final leg of the Suicide Mission, and the pilot who always had Shepard's back no matter what, is now suddenly fleeing the Earth battle for an unexplained reason, and gets the ship trashed as a result. Character Derailment, much? The Extended Cut attempts to resolve this issue, via a squadmate telling Joker it's time to go, but the point still stands.
The derailment is even worse if the squadmate telling Joker to leave Shepard behind is his/her Love Interest. So much for "No One Left Behind," huh?
The "Synthesis" ending amounts to Shepard forcing all organics to become half-synthetic beings against their will (basically, what Saren wanted to do in the original game writ large). The mechanics or consequences of this choice are never dealt with, yet this is apparently presented as the "best" option to pick, as it requires the highest amount of Effective Military Strength to get access to. In effect, it seems to be arguing that Saren was right all along... and, therefore, Shepard's entire struggle from Eden Prime onwards was not only pointless but also "wrong" and thus put the entire galaxy in a worse position. (Facepalm) Seriously?
Also in the Synthesis ending is a substance that reduces/increases the mass of objects when electrically charged or fast computers allow a fusion of synthetic and organic life without having any equipment that could make that happen in the area for any of it. Every other tech in the game came from two sources: mass effect or fast computers.note One exception, Medi-Gel came from genetic engineering. Neither of those allow for what the ending makes happen (without a lot of equipment for each life form). It happened to Shepard in ME2 but that took a lot of tech working on Shepard to do it.
The Destruction ending destroys all Reapers. But for some reason it also destroys all artificial intelligence life, including the Geth, but apparently has no ill effect on organic life and seems to cause no lasting damage to regular machines because... of reasons that are never explained in any waynote It does do damage if you don't have a high EMS but there is no explanation for why that matters when you might not have even sent any resources to the Crucible project.
What's worse is that they could have just said that the Crucible will fry all Reaper-based technology. Given that 1: most technology is based on stuff the Reapers left behind, and 2: EDI and the Geth currently use Reaper Code to achieve full sentience, there were a couple of plot holes that could be easily filled.
Drew Karpyshyn, the writer for Mass Effect and co-writer for Mass Effect 2 actually wrote an ending for the game that would have made sense and tied into the foreshadowing about Dark Energy, and would have offered a meaningful, difficult choice where Shepard has to either destroy the Reapers even though they're probably the best hope for the galaxy surviving the singularity, or side with them because as horrible as their methods and actions are, they may be the only real hope the galaxy has. This was tossed out in favor of a nonsensical rant about how AI's are evil (despite the first game foreshadowing that they weren't, the second game outright demonstrating it, and the supposedly safe, non-sapient VIs having a worse track record for going rogue and killing people).
On top of that, the player isn't even able to throw the resolved geth/quarian conflict (if they got the Golden Ending in it) as evidence that Synthetic and Organic life can co-exist peacefully - even if it got brushed off with "What happens a century from now? A millenia? 10 millenia? You do not know - we do", it would at least address the issue!
In the Extended Cut, the final scene of the Refusal ending (which replaces the Stargazer with a female talking to the child) handwaves the entire next galactic cycle and says that, "Hey, we managed to beat the Reapers anyway thanks to this datapad", completely marginalizing the struggle Shepard and company put up with for three games.
Jacob Taylor, the sane, lacking-psychological-issues-unless-you-count-his-father romance option from Mass Effect 2, becomes romantically involved with a scientist named Dr. Brynn Cole (who is voiced by the same woman who played female Hawke in Dragon Age II. In fact, Jacob and Brynn are even going to have a child together. If you're a male player, you'll probably be happy for Jacob. If you're a female player, you'll also probably be happy for Jacob unless you romanced him! If you did, he cheats on you and hooks up with Cole anyway. This happens with no one else; for example, Garrus can hook up with Tali, but not if you romanced him. Even worse - if a female Shepard who romanced Jacob talks to Cole and chooses specific dialogue, Cole's dialogue comes across as passive-aggressive, and makes Shepard out to look like someone who can't even talk back. This was later addressed in the Citadel DLC, where FemShep has the opportunity to confront (and potentially slap) Jacob about the whole situation.