Mass Effect sets up several large plot points that carry over into the remainder of the trilogy, and player's choices can have a lasting impact on the events of Mass Effect 2 and Mass Effect 3. But not every story element is kept consistent throughout the series. Mass Effect has a few big plot holes that just don't make sense.
Some of the plot holes in the Mass Effect trilogy are likely writing decisions that changed with time. Developers may have found the storyline moving in a different direction than was originally planned as time went on. Others might have been contributed to the reception certain aspects of Mass Effect received when it was released.
A few of the plot holes in the Mass Effect series result in some players feeling that their choices don't actually matter. Certain major events in the series will occur regardless of player choices, even if the game has alternate methods of explaining how they happen. These explanations don't always make complete sense and can leave the plot feeling poorly patched up.
Mass Effect 1's Biggest Plot Holes: The Beginning of The Reapers
On Virmire, Shepard is able to directly communicate with Sovereign. This is the first time in the Mass Effect series that players are able to interact with a Reaper, so while it's likely that this plot hole can be attributed to story specifics evolving with time, it's still inconsistent with later games. Sovereign claims that the Reapers have no beginning and no end - and while this might be a case of an unreliable narrator or an intimidation tactic, it contradicts information that Shepard finds out later on in the Mass Effect series. Players learn that Reapers were created by the Catalyst in Mass Effect 3, which was constructed by the Leviathans, meaning that the Reapers actually do have a definitive beginning.
Mass Effect 1's Biggest Plot Holes: The Virmire Genophage Cure
Also on Virmire is a Krogan breeding facility in which Saren is able to create Krogan soldiers by, according to the Salarian, finding a cure to the genophage. This is one of few areas in Mass Effect in which players have little-to-no choice in the outcome of the situation. The cure will be destroyed regardless of Shepard's actions in Mass Effect - and while this is done to prevent Saren (and the Reapers) from using the Krogan as weapons, it doesn't make sense that the data couldn't be saved and studied. In later Mass Effect games, similarly dangerous tech can be salvaged and used regardless of risk, making the lack of freedom in preserving the Virmire cure inconsistent with the rest of the trilogy.
Mass Effect 1's Biggest Plot Holes: The Rachni Queen & The Breeder
In Mass Effect, Shepard has the option to either spare or kill the Rachni Queen. Later on, in Mass Effect 3, players will encounter versions of the Rachni that have been indoctrinated by the Reapers. It's revealed that these are products of a creature called The Breeder, who is nearly identical to the Rachni Queen. If she was spared, the explanation is obvious - the Reapers used her to create more Rachni. However, if the Rachni Queen was killed in Mass Effect, this plot point makes less sense. The Breeder is supposedly made up of various Rachni children instead - but that isn't reflected in its design.
Regardless of why these plot holes occurred, fans of the series may find them distracting as they play through the trilogy. But despite the sometimes inconsistent nature of its story, Mass Effect still manages to provide players with a fulfilling and interesting narrative.