Before the story starts, two things must be determined. Shepard's background:
• Spacer: Shepard was raised on ships and space stations by his Alliance soldier parents.
• Sole Survivor: Shepard's unit fell to a thresher maw attack on Akuze, leaving Shepard to fight for survival against all odds on his own.
Shepard's Morality

Noveria: Administrator Anoleis

Searching for Saren on Noveria, Shepard lands the Normandy in Port Hanshan. The place is in lockdown due to bad weather, on Administrator Anoleis' orders. Shepard need to grab a garage pass before they can follow Saren. There are several ways to do this:
• Gianna Parasini, Anoleis' administrative assistant, at one point reveals herself as an undercover investigator trying to prove Anoleis' corruption. In exchange for convincing Lorik to testify against Anoleis, Parasini hands Shepard a garage pass.
Noveria: The Rachni Queen

On Peak 15, Binary Helix, a corporation controlled in part by Saren, has been cloning Rachni, a long-disappeared race of deadly insectoids. Saren plans to use the cloned Rachni as soldiers. Their queen can be found after dealing with Matriarch Benezia, Saren's assistant. The queen can either be destroyed outright, or let go.
Feros: Zhu's Hope

Shepard arrives on Feros, looking to investigate why Saren sent Geth to attack the planet.
• Exogeni Corporation, the people who founded Zhu's Hope, the Feros colony Shepard landed the Normandy at, have ordered their local representative, Ethan Jeong, to purge the colony to get rid of any evidence of their practices. When he wouldn’t back down Shepard simply shot him.
• The Thorian, an ancient mind-controlling creature living under Zhu's Hope, has taken control of the colonists who need to be neutralized somehow. Shepard incapacitated them with melee attacks and special nerve gas grenades.
• The Thorian has also been using a green-skinned Asari as a template for cloned soldiers. Shepard let her go.

A group of batarian terrorist hijacked an asteroid, and are trying to crash it into the human colony world of Terra Nova. Their leader, Balak, when confronted, offers Shepard a choice: either let him go, or fight him at the cost of the lives of his hostages, whose cell he has booby-trapped with explosives.
Virmire: Wrex

Shepard travels to Virmire in search of a Salarian recon team who has information on Saren. Here, it is revealed that Saren has found a cure to the Krogan's artificial genetic disease, the Genophage, and is using it to breed an army of Krogan. They agree that the cure needs to be destroyed, but Wrex, Shepard's Krogan squadmate, is furious at this. He is convinced to follow Shepard into battle.
Virmire: Ashley or Kaidan

Shepard and the crew plant a bomb in Saren's facility to destroy it. Squadmates Kaidan and Ashley play important roles here: one of them leads the Salarian recon team, while the other arms the bomb. The Geth begin to overwhelm the two groups, and Shepard needs to decide whether to save Ashley or Kaidan. The one left behind, Kaidan, dies in the bomb blast.
Saving the Council

In the battle for the Citadel at the end of the game, the fleet's flagship, the Destiny Ascension, with the Citadel Council on board, gets under a lot of fire from the Geth attackers. Shepard orders the fleet to assist the Destiny Ascension, saving both the ship and the council.
The New Council

• The council is saved, and they offer humanity a seat. Shepard has to name either Udina or Anderson humanity's representative and goes with Udina as he is a politician.
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Mass Effect 2
Veetor

Shepard heads to the human colony of Freedom's Progress to find out what happened to its inhabitants, who suddenly disappeared. They are met with resistance from the colony's mech defense force. Veetor, a Quarian, who gave the mechs the command to attack because he feared for his life, is confronted at the end of the mission. He is sent back to the Migrant Fleet to recover.
Loyalty: Mordin

Mordin has to head to Tuchanka, the Krogan homeworld, to rescue a former colleague of his, Maelon, with whom he has worked on the Genophage. There, he discovers that the mercenaries who took him didn't actually take him; he agreed to work with them on a cure, out of guilt for what he's unleashed with the Genophage.
• At this point, Mordin will try to shoot Maelon. Shepard convinces him not to.
• Then, Shepard can decide what to do with Maelon's data. Mordin saves it.
Loyalty: Jacob

Jacob receives word of a distress call originating from the planet Aeia, where the ship his father, Ronald Taylor, served on crash-landed. While exploring the crash site, Shepard and Jacob discover that at one point, the ship's officers and crew were divided into two groups, with the officers hoarding all the food. The crew had to survive on the toxic plantlife, which eventually rendered them either amnesic or insane. Ronald, the only officer left, ruled over the survivors using the remaining mechs. Eventually, Shepard and Jacob confront him.
• Ronald is left on the planet at the mercy of the remaining crew, potentially with a gun he can use to commit suicide before the crew can get to him.
Loyalty: Miranda

Miranda's father is planning to kidnap her sister, Oriana, and she asks for Shepard's help with getting rid of her kidnappers. They ultimately succeed, and Oriana can continue her life. Miranda can be convinced to give up the facade and reveal herself to Oriana, eventually having a relationship with her sister.
Loyalty: Jack

Jack travels to Pragia, where she was experimented on by Cerberus as a little girl. There, they find Aresh, a fellow survivor of the experiments who plans to restart the facility. Shepard can convince Jack to kill Aresh.
Loyalty: Garrus

Garrus finds out that Sidonis, the man who betrayed him and got his team killed on Omega, is on the Citadel. He asks Shepard to help lure him out and kill him. Shepard allows him to be killed.
Loyalty: Samara

Samara asks for Shepard's help with tracking down her Ardat-Yakshi daughter, Morinth. Since Ardat-Yakshi are essentially vampires, and huge dangers to society, she needs to hunt her down and kill her. Eventually, Samara and Shepard confront Morinth. Shepard can decide to help Morinth, which results in Samara's death. Samara kills Morinth, making the mission a success.
Loyalty: Tali

Tali has been sending Geth components to his father for research purposes. Unfortunately, the Geth awaken and slaughter the research team, along with Tali's father. Tali gets charged with treason for smuggling Geth into the Quarian fleet. To clear her name, Shepard and Tali search the research ship, and find evidence that can prove Tali didn't do anything wrong, but would condemn her father. Shepard and Tali meet the Admiralty Board shortly after to discuss the charges.
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• Shepard gave a speech, persuading the Board that a person like Tali would never be able to betray her own people. This way, Tali's name is cleared and her father's reputation is preserved.

Loyalty: Legion

Legion tells Shepard that the Geth heretics, a faction of Geth fought in Mass Effect 1, are trying to convert the other Geth to the Reaper cause by unleashing a virus into the collective from a space station. Eventually, the virus is stopped—at that point, Shepard needs to decide to either rewrite the heretics' behavior to strengthen and unify the Geth, or destroy the station, and the heretics with it. Shepard decides to destroy the heretics.
Loyalty: Zaeed

Zaeed's mission takes him and Shepard to a refinery on Zorya, which has to be liberated from Blue Suns, a group of mercs Zaeed has co-founded. While there, they find Vido Santiago, long-time rival to Zaeed and the other co-founder of the Blue Suns. The two get in a gunfight, with Zaeed shooting a gas pipe and unleashing an explosion, injuring Vido. This starts a chain reaction which threatens to destroy the refinery and kill its workers.
• Shepard chooses to chase Vido, the refinery workers all die, but Zaeed is able to kill Vido.
Loyalty: Kasumi

Kasumi goto asks for Shepard's help with retrieving something from Donovan Hock, an arms dealer who's killed her partner, Keiji. The object in question is a greybox, which stores Keiji's memories. After finding and examining it, Shepard and Kasumi discover that there is a lot of sensitive information within which, if found, could be very dangerous in the wrong hands. However, Kasumi is reluctant to destroy the greybox due to her ties with Keiji. Shepard convinces her to destroy it.
Overlord: David Archer

Shepard and the Normandy's crew are sent to investigate a Cerberus station which has ceased all communications with the outside world. There, they find that David Archer, the autistic brother of one of the researchers, Gavin Archer, has been merged with a Virtual Intelligence program designed to control Geth. The VI program goes rogue and the Geth control group begins destroying the station. Shepard eventually finds David deep within the laboratory, hooked up to painful-looking machinery, with his brother watching over him.
• Shepard takes David from Gavin to prevent any further abuse, and send him off to Grissom Academy, a school for gifted youth.
Confrontation: Jack Vs. Miranda

At one point, Jack will get into an argument with Miranda, who refuses to admit that what Cerberus did to Jack when she was a child was wrong. Shepard convinces them both to put aside their differences for the mission.
Confrontation: Legion Vs. Tali

Like Jack and Miranda, Legion and Tali also have a fight. Tali finds Legion accessing her omni-tool and trying to send Quarian data to the Geth. Legion insists that he's doing this only to help keep his people safe. Shepard interferes and Legion agrees not to send any sensitive data to the Geth, and Tali decides to help him.
Saving the Normandy's Crew

While Shepard is away on a mission, the Normandy comes under attack from a Collector cruiser, and her crew, save for Joker, is taken. Shepard has to decide whether to go after them immediately, or delay and do a few more missions first. Shepard saves the entire crew.
Choosing the Team

Throughout the Suicide Mission through the Omega Relay, Shepard needs to assign squad mates to various tasks, to be carried out within and around the Collector Base. Some are better fit for biotics, others for natural leaders. All squad mates survive the suicide mission.

Destroying the Collector Base

At the end of the final mission, Shepard is contacted by the Illusive man, who says the technology on the Collector Base could be used against the Reapers. Shepard has to decide whether to keep the Base, merely setting off a radiation pulse to kill the Collectors, or destroy it. Shepard chooses to use the radiation pulse and save the collector base.
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Mass Effect 3
Diana Allers

On Shepard's first visit to the Citadel after the Reaper attack on Earth, they're approached by Alliance News Network correspondent Diana Allers. She wants to join the Normandy's crew to report from the front lines of the Reaper war. Should Shepard say yes, she will move onto the Normandy and will occasionally interview crew members (and Shepard). Otherwise, she joins another ship. Throughout the events of Mass Effect 3 Diana is embedded on the Normandy.

Jack's Students

Shepard investigates Grissom Academy after finding out that they're under Cerberus' attack. After evacuating the students, Shepard can decide where to send Jack, who works as an instructor there, and her class. They can be used as support for other troops, which is safe, or sent off to the front lines to fight, which is considerably more dangerous. Shepard chooses to have them at the front.

The Rachni Queen

A Krogan team has gone missing, and Shepard is tasked with finding it. They are found on the planet Utukku, under attack by Reaper-controlled Rachni. Grunt, the Krogan squad mate from the second game, is leading them. Shepard and the Krogan fight their way to the source of the Rachni, the Rachni Queen. Shepard has to choose between saving the Rachni Queen by sacrificing the Krogan team, or leaving the Queen to die and rescuing the Krogan team instead. Shepard saves the Rachni Queen, Grunt is the only survivor from the Krogan team.

Samara's Fate

Shepard searches for a vanished Asari commando unit who went to answer a distress call from an Ardat-Yakshi monastery. There, Shepard finds Samara, who is searching for her two other Ardat-Yakshi daughters, Rila and Falere. Rila ultimately stays behind to detonate a bomb left behind by the commando unit to destroy the monastery, which is now filled with Reaper-indoctrinated Ardat-Yakshi. Shepard, Samara and Falere manage to escape—however, Samara's Justicar code disallows her from letting Ardat-Yakshi run free. Because she would have to kill her own innocent daughter, she resolves to commit suicide. Shepard lets Samara pull the trigger. Afterwards, Falere is deemed a risk and killed.

The Volus Fleet

Shepard is asked to investigate Din Korlack, the Citadel's Volus ambassador, for ties to Cerberus. He is found captured by a group of bounty hunters, Zaeed Massani among them. Shepard and Zaeed rescue Korlack, who tells them that Cerberus plans to attack a Turian colony. He refuses to reveal which one, however, afraid that Cerberus will find him. Instead, he offers the support of the Volus fleet against the Reapers. Shepard was persuasive enough to get both the location of the colony and the fleet's support.

Krogan Vs. Salarian

Before taking on the mission to supply the cure to the Genophage to the Krogan, Shepard is approached by the Salarian Dalatrass. She reveals that the Shroud, the facility used to disperse the cure, has been sabotaged by the Salarians to prevent a cure from being distributed. She offers her co-operation in the war effort in return for Shepard making sure the sabotage remains hidden.
Shepard tells Mordin about the Dalatrass' plan. He disperses the cure over the planet, sacrificing himself in the process, securing Krogan support for the Reaper war, but losing the Salarians.

Geth Vs. Quarian

Shepard's orders take him to the Perseus Veil, to help the Quarian Migrant Fleet fight against the Reaper-controlled Geth forces. Eventually, Shepard finds Legion on the Geth flagship, who is being used to transmit the Reaper signal to the Geth against his will. After purging the Reaper code from the Geth collective and destroying the Reaper base on Rannoch, the Quarian homeworld, Legion tells Shepard that he plans to apply his own version of the Reaper code to the Geth, in an effort to achieve true intelligence. Tali is very much against this.
Shepard negotiates a ceasefire. The Migrant Fleet stands down, and the Geth join the Quarians in repopulating Rannoch.

has two choices: talking her into going to prison peacefully, or killing her.
Control, Synthesis, Destruction, Refusal

I would like for the ending to have actually been that they destroyed the Reapers and lived to tell the tale…I didn’t like any of the endings even in the extended cut. All of the above events are open to be changed if you would like to play with an alternative choice.