With Deus Ex writer Mary Delmarle officially ing Mass Effect 4 team, fans are likely ing a few of the discrepant moments in the original trilogy. The truth is, there are many, and they are strange.
Mass Effect Legendary Edition gave the series a much-needed visual glow-up. Unfortunately, it couldn't do much for some of the nonsensical plot that Commander Shepard and their team had to wade through to make it to endgame. From odd choices made following the Eden Prime debacle to Spectre status not amounting to a hill of beans, there are many aspects that left players scratching their heads in sheer confusion.
First Hearing Of The Council
Shepard and their crew are brought before the Council shortly after arriving on the Citadel to report on the events on Eden Prime. They report that the Spectre agent Saren murdered Spectre agent Nihlus and had evidence through a traumatized dockworker/smuggler. They also accused him of being responsible for the destruction of the Prothean beacon.
All of this evidence is written of as either circumstantial or unreliable, which makes sense. What doesn't make sense is Anderson's sudden idea to claim that Shepard's vision validates anything. Not only did that make humanity look like a joke, but the following childish temper-tantrums from Udina, Anderson, and even Shepard made more than a few palms smack into foreheads.
Tali's Luck With Geth
Evidence of Saren's corruption is found when Shepard rescues Tali from a group of thugs hired by Saren to shut the quarian up. Tali takes her evidence to the human embassy where she reveals that she was able to retrieve a recording of Saren talking treasonously to an accomplice. This evidence in turn sways the Council to revoke Saren's Spectre status and declare him a fugitive.
This one is easy to overlook as needing to advance the story along quickly, however the method in which this is handled is convoluted at best. There are no documented records of anyone, not even a likable squate like Tali, being able to successfully decrypt a geth data module before it self-destructs. She just happens to be the deus ex machina of quarians who just happened to find the one geth with that specific recording.
Second Hearing Of The Council
At the second hearing, the Council accepts that Saren has gone rogue, declaring that vocal recognition was irrefutable. He is stripped of his Spectre status and Shepard is inducted as the first human Spectre. His accomplice is also identified when talking about Reapers and The Conduit. This is where the conversation makes for some head-scratching.
Salarian Councilor Valern comments on his curiosity about what the Reapers are, but less than 30 seconds later, after hearing a mere theory, he writes it off as a red herring as though he hadn't been the one voicing curiosity. On top of that, Councilors Sparatus and Tevos claim the Reapers were invented to specifically throw Shepard off. This would make sense if Saren were psychic. But he's not.
Shepard's Spectre Status Is Meaningless
The Spectres are an elite force of law enforcement chosen by the Council from the best individuals the galaxy has to offer. They are picked specifically from races who have representation on the Citadel Council and are the first line of defense in a galactic emergency. They typically operate outside the law and have complete discretion in how they carry out their missions.
Shepard became a Spectre during the Council's second hearing. However, attempts to invoke their status are stunted all throughout their journey. They are forced to follow the rules of Noveria and threatened when defending a quarian migrant. The indentured servant on Illium could have been freed instantly. Effectively, anytime Spectre authority could be used to push through an inconvenience, Shepard seems unable to use it.
Council's Dismissive Attitude
After Shepard is resurrected by Cerberus, they travel to the Citadel to implore them to help stop Collector attacks on human colonies. The Council told Shepard that those colonies were not subject to Council protection. They do offer to reinstate Shepard as a Spectre (provided Shepard made the important choice to protect original Council) as a silent show of for Shepard's quest against the Collectors.
Two things that cause confusion are the victim-blaming comment "humanity knew the risks" and the incredulous dismissal of the Reaper threat. The snub against humanity was bad enough, but to dismiss the Reaper threat despite the evidence is nonsensical. It would have been more acceptable to say they wanted to avoid galactic panic and investigate quietly. Instead, they rather smugly declared the threat a myth.
Miranda Claims Second-In-Command
When Jack is recruited to the Normandy team, she is immediately set upon by Miranda who tells her that orders given were orders to be followed. Out of the blue, she claims that she is Shepard's lieutenant. Jack, being the rebel criminal she is, brushes Miranda's comment off her shoulder before leaving the conversation for the lower decks.
This is more annoying than confusing, but it still makes little sense. For one, it's typical of a ship's captain to choose their seconds. For two, Miranda being the Illusive Man's direct makes her a conflict of interest when Shepard gives orders. Certainly, if the option had been made available, Shepard would have chosen Garrus as their loyal lieutenant.
Kaidan/Ashley Distrusts Shepard
Depending on who survived the bombing of Virmire in Mass Effect, either Kaidan or Ashley will encounter Shepard after they defeated the Collectors on Horizon. The former crewmate chastises Shepard for ing Cerberus, reminding the commander of all the illicit activities the organization was involved in. They go so far as to accuse Shepard of betraying the Alliance before departing company.
The issue here is Shepard had met with David Anderson long before they ran into Kaidan/Ashley. Anderson outright tells Shepard that Kaidan/Ashley are on a secret mission, which indicates that he has some way to communicate with them. Anderson would have surely informed Kaidan/Ashley of Shepard's situation and thus avoided the rather uncomfortable argument between friends.
Thessia
The homeworld of the asari was hit by Reaper forces with intense brutality. It was this attack that prompted Councilor Tevos to give in and inform Shepard of an asari artifact that could in fact turn the tide of the war. Shepard makes Thessia a priority mission and fights through hoards of Reaper forces to obtain the artifact.
Shepard and crew make it to the temple. However, they soon discover that the scientists they were to meet were killed by the Cerberus assassin Kai Leng. This discovery is followed by a battle against Leng that Shepard legitimately wins, however, that victory is unjustly and nonsensically revoked in a cutscene where Shepard goes from competent soldier to flailing rookie.
The Catalyst
An artificial intelligence housed somewhere on the Citadel, the Catalyst is the reason the Reapers exist in the first place. It was itself created by the Leviathans in an attempt to protect organic life at all costs. The Catalyst deemed the only way was to harvest organics and create the Reapers in a never-ending cycle. This is all well and good story-wise, but what doesn't make sense is how it appears to Shepard.
The Catalyst takes the form of a boy Shepard could not save at the beginning of Mass Effect 3. This makes no sense because why would Shepard care more about this kid than the people they served with and lost throughout the series? Wouldn't the Virmire casualty make more sense? This boy meant nothing to Shepard, yet they are tormented by him almost every night.
The Crucible's Non-Prejudiced Targeting
Of all the confusing things in Mass Effect, the Crucible's indiscriminate destruction is by far the worst. In the final scene, Shepard is given three choices (four if you count not choosing at all): Destroy, Control, or Synthesis. Shepard can assume direct control of the Reaper forces, or synthesize organic and synthetic life. Destroy, however, will destroy all synthetic life be it Reaper, geth, AI, VI, or cybernetic implant.
This makes no sense as the Normandy is equipped with a Reaper IFF device that identifies Reaper forces from allies. Because it is a program, it can be copied and installed onto any ship or computer. Joker at one point even states in Mass 3 that the IFF is running. The galaxy could have been spared the loss of so much tech had they considered the IFF.