For the purposes of this game the following represents the key choices made by Commander Shepard in the Mass Effect Trilogy of games and is considered canon for the game:

Shepard’s Service History

Shepard is a compassionate Paragon throughout the events of the Mass Effect trilogy.

Spacer: Shepard was raised on ships and space stations by her Alliance soldier parents.

War Hero: Shepard, at one point, risked her life to save fellow soldiers, and single-handedly dealt with a Batarian attack on Elysium.

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. Shepard can’t bring herself to be party to genocide and let the queen go.

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 and the commander doesn’t have to kill him.

Virmire: Ashley and Kaiden
While on Virmire Shepard had the unenviable choice of being only able to save one of two of her crew mates, her choice was and unenviable one and ended up choosing Ashley letting Kaiden perish.

Saving the Council

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 ordered the fleet to assist the Destiny Ascension, saving both the ship and the council. Many humans die to save the council.

Choice of Humanities Citadel Council member Captain Andersen or Ambassador Udina

Being the hero of the Citadel by defeating Sovereign and Saren shepard is given the ability to choose humanities representative to the Citadel Council. Shepard chooses her mentor Admiral Andersen to represent humanity on the Citadel Council.

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 tried to shoot Maelon but Shepard convinced him not to. Then, Shepard decided what to do with Maelon’s data. Mordin was told to save it.

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 decided to rewrite the heretics’ behavior to strengthen and unify the Geth, instead of destroying the station, and the heretics with it.

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 decided to destroy the Base, In the end letting Miranda to cut the Illusive man off and giving her his resignation.

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. Shepard and the Krogan fight their way to the source of the Rachni, the Rachni Queen Shepard saved earlier. Shepard again chooses to save the Rachni Queen by sacrificing the Krogan team. The Queen and the Rachni aid in creating the Crucible.

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 told Mordin about the Dalatrass’ plan, though Mordin realized there is something wrong with the Shroud by himself. He dispersed 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 was very much against this.

But Shepard negotiated a ceasefire. The Migrant Fleet stood down, and the Geth joined the Quarians in repopulating Rannoch.

Control, Synthesis, Destruction, Refusal

At the end of the third game, on the Citadel, Shepard met the Catalyst, the AI in control of the Reapers. It said that Shepard was the first organic to ever be able to reach it, which meant it has to rethink its solution to the chaos of organic life: wiping out organics and saving them in Reaper form, each time galactic civilization reaches its peak. However, he cannot make any changes without Shepard’s help.

Shepard destroyed vital equipment on the Citadel, which sends a pulse through the mass relays, reaching everywhere in the galaxy. The pulse damages the mass relays and, were it not for an unknown Geth who sacrificed himself to rewrite the Catalyst, would have destroyed all synthetic life in the galaxy, rather than just The Reapers and their Indoctrinated.