A large part of what makes Mass Effect such a riveting game series is a complex storyline that focuses on choice. At key points throughout the trilogy, players are forced to weigh difficult decisions and decide on the best course of action, sometimes with little guidance. Some choices are right, others wrong, and the rest are no-win scenarios.

RELATED: All 10 Romance Options For Ryder In Mass Effect: Andromeda

That being said, certain choices in the games are far more difficult than others, and can easily lead to a crisis of conscience for the player. These choices often led to bittersweet outcomes at best, while others require players to complete certain parameters and develop a high reputation to open up better options.

Sparing Or Killing The Rachni Queen (Mass Effect)

Rachni Queen attacks in a cave in Mass Effect Legendary Edition

One of the greyest of Mass Effect's narrative forks is the decision to either spare the Rachni Queen, or doom her species to extinction. At first, it may seem like an easy call, except for the fact that the Rachni are presented as rather terrifying antagonists in the vein of the xenomorphs from the Alien franchise.

However, the Rachni Queen does make her case for being spared, and it's up to players to decide whether to put her down, or allow her to live. The latter puts the entire galaxy at risk of another horrifying war against the species, but it may also pave the way for one of Mass Effect's best choices in the entire trilogy.

Wrex And The Genophage Cure (Mass Effect)

Ashley and Wrex point guns at each other in Mass Effect Legendary Edition

Wrex is a powerful tank who comes in handy during a fight, and he's a cool character to boot, so it's wise to have him tag along. However, players will have to make a grueling decision whether to kill him or convince him to stand down during the mission on Virmire. The former is one of Mass Effect's worst choices, as it robs the story of a wonderful character.

The standoff occurs when lead antagonist Saren is revealed to have a cure for the Genophage, a genetic virus preventing the Krogan species from reproducing at a normal rate. With his species facing extinction, Wrex will attempt to strongarm Shepard into doing what he wants, but it will come at a cost.

Destiny Ascension Vs. Sovereign (Mass Effect)

A robot monster sttacks a city or something in a Mass Effect game.

The ultimate battle against the Reaper ship Sovereign at the end of the first Mass Effect game comes with a hefty price tag attached to it. During the battle, players must decide whether to direct the Alliance Fleet towards saving the Destiny Ascension, or turning their combined firepower on Sovereign.

If players choose the latter, the Citadel Council will be slaughtered, which will have huge ramifications for the story as it moves forward. The Destiny Ascension also won't be present during the final battle against the powerful and mysterious Reapers in Mass Effect 3. 

Kaiden Vs. Ashley (Mass Effect)

Mass Effect's Kaiden or Ashely Who Has The Better Story Arc

Perhaps no other choice in the Mass Effect trilogy is as grueling and heartbreaking as this one. It all boils down to how each player feels about squad mates Kaiden and Ashley, and things get a lot more complex if they pursue a romantic relationship with either one.

RELATED: 10 Memes That Sum Up The Mass Effect Franchise

There are reasons for sacrificing one to save the other, but one thing is for certain - no matter what decision the player makes, there's no going back. The dead character will be absent from the next two games in the Mass Effect trilogy, which will be referenced in the story.

The Heretics (Mass Effect 2)

Mass Effect Geth

Mass Effect 2's storytelling prowess was significantly better than the game that preceded it, with the writers ratcheting up the discomfort over the game's key choices. It occurs when the character Legion finds a faction of its fellow Geth, which chose to side with the Reapers.

The choice is simple - reprogram the faction to be loyal to humanity, or eliminate them as a threat. The choice focuses largely on how each player identifies with the Geth as a race, and whether they base their decision on human equivalents, as opposed to technological beings.

Scheduling The Crew Rescue (Mass Effect 2)

The Normandy Crew held hostage in Collector pods in Mass Effect 2

First time Mass Effect players should be especially wary of this one, as it can have dire consequences moving forward. There will come a point in the game when the dreaded Collectors attack the Normandy and kidnap her crew, forcing Shepard and team to launch a daring rescue mission.

However, if players dilly-dally by engaging in side missions or other endeavors, the chances of their survival plunge. It's advised that players tidy up their mission roster throughout the game, so as not to fall victim to this unfortunate outcome.

The Suicide Mission (Mass Effect 2)

The final battle against the Collectors in Mass Effect 2 is dubbed "the suicide mission" for a reason. It's one of the most heart-pounding moments in the entire trilogy, and can end with the deaths of nearly all of Shepard's squad members, depending on a set of decisions.

Players will have to exercise great care and common sense when it comes to assigning directives to each squad member. Failure to capitalize on their strengths could put them at death's door, leading to massive casualties. This has huge ramifications for the overall story in Mass Effect 3. Luckily, best companion candidate Liara Tsoni is not present during the battle, which means there's no danger of losing her.

Quarians Vs. The Geth (Mass Effect 3)

Another knuckle-biting Mass Effect decision takes place in the third game, when tensions between the Quarian and Geth races boil over to the point of disaster. Most players will be forced to choose whether to let the Quarians die, or wipe out the Geth, both of which have consequences.

RELATED: Shepard's 10 Best Romances In Mass Effect, Ranked

However, there is a third option locked behind a specific set of criteria that must be met. If that option is available, players can broker peace between the two races, rather than get stuck in the middle of a choice with no positive outcome.

Mordin Vs. The Genophage Cure (Mass Effect 3)

Mass Effect Mordin Smiling

Mordin is one of the quirkiest, yet simultaneously devious characters in Mass Effect, with a moral compass that is ambiguous at best. His work on the controversial Genophage program makes him something of a wild card when it comes to decision-making within the game.

Players will need to decide whether to skip curing the Krogan race of the Genophage, or leave them to their doom by saving Mordin. It's a difficult choice, particularly because of the inherent threat the Krogan pose to the galaxy if their numbers are ever replenished.

The Final Decision (Mass Effect 3)

Mass Effect 3 Original Ending Missing Legendary Edition

Mass Effect 3's ending is one of the most controversial in gaming, with no real "good" outcome to speak of. Instead, it all boils down to one of three scenarios, each of which have their benefits and drawbacks. That being said, none are particularly satisfying.

Be that as it may, a decision does need to be reached, and it'll boil down to each player's sense of ethics and morality, as well as their overall vision for the galaxy writ large. In fact, ME3's ending was so polarizing that Mass Effect: Andromeda was forced to take place in an entirely different galaxy, just to escape the ramifications of this choice.

NEXT: 10 Ways Mass Effect: Legendary Edition Is The Best Introduction To The Franchise