Major Plot Decisions
■Rescuing Kaidan Alenko or Ashley Williams during the Virmire mission.
The character who was left behind will not appear in any subsequent games in the Mass Effect series. It is a permanent character death.
■Killing Wrex during the Virmire: Wrex and the Genophage confrontation.
If Wrex survived, he returns to Tuchanka and has united all the krogan under Clan Urdnot to combat the genophage and strengthen the krogan. If Wrex is killed (or if the player doesn't import), the more traditional Urdnot Wreav becomes the leader of Clan Urdnot, and little changes for the krogan.
■Deciding the fate of the Council during the battle with Sovereign, and the nomination of either Captain Anderson or Donnel Udina to the Council.
If the Council is saved with Anderson as a representative, Shepard is granted an audience with the Council and has the opportunity to be reinstated as a Spectre. All other options will result in no audience with the Council, but Shepard will still be reinstated as a Spectre if either Anderson was made a Councilor (even if the original Council was lost) or if the Council was saved (but Udina was made the human Councilor). If the Council was not saved, aliens you meet on on the Citadel will be somewhat bitter against humanity, and Avina will have a fascist streak, repeatedly notifying Shepard that certain inquiries have been forwarded to C-Sec, and to surrender if approached for arrest.
Other Plot Decisions
■Fist on the Citadel
If Fist is spared, Shepard encounters him at Afterlife, where Fist angrily admonishes Shepard for ruining his life and making the effort of harassing him across the galaxy despite him being a small time criminal.
■Colonists and Shiala on Feros
If sufficient numbers of colonists survived (or if Shepard persuaded Ethan Jeong to commit ExoGeni resources toward rebuilding the colony,) Shepard encounters a representative of the colonists on Illium who need help extricating themselves from a medical contract. If Shiala was spared, she is the representative. (Note: Even if the Thorian enslaved colonists are killed but Shiala is spared, Shiala still references Shepard saving them.)
■Rachni Queen on Noveria
If the Rachni Queen is set free, she will send a message through an asari on the planet Illium conveying her gratitude, with further dialogue ensuing. There is a news report of small scout ships seemingly rachni in design that, when approached, quickly retreat. If the Rachni Queen is killed, Galactic News will instead report of data recovered from Peak 15 linking to cloning of rachni, but no rachni found.
■Gianna Parasini on Noveria
If Shepard aided Gianna, she is found on Illium where she again requests help, and will buy Shepard the promised beer. If a male Shepard aids her, she will additionally give him a kiss. This quest also appears in Mass Effect 2 without an imported save file, or on an imported save file where you got what you needed via another method that does not involve Gianna, but male Shepard will not be able to receive a kiss.
■Encouraging Garrus to be more renegade or paragon
If Paragon, Garrus will have attempted to join C-Sec but lament that he could do little good there in the chaotic aftermath of the attack on the Citadel; during his loyalty mission, if Shepard questions his plan he will say that killing Sidonis is something he must do. If Renegade, Garrus will have trained to become a Spectre but will claim that it never worked out; during his loyalty mission, if Shepard questions the plan Garrus will be confused.
■Helping Tali with her personal pilgrimage quest
When first encountering her on Freedom's Progress, mentioning the gift of the geth data can serve to prove Shepard's identity. This will also change the dialogue at the end of the encounter if that particular dialogue choice is selected.
■Rana Thanoptis on Virmire
If Rana is spared, Shepard encounters her during Grunt's recruitment mission on Korlus while seeking Okeer.
■Captain Kirrahe on Virmire
A dialogue option will open during which Mordin Solus will reference Kirrahe's "Hold the Line" speech during ship conversation if a Mass Effect save is imported. The dialogue will change slightly depending on whether or not Kirrahe survived the mission.
Assignment Decisions
These result merely in e-mail to private terminal or news reports unless noted otherwise.
■Shepard's resolution of the pre-service history quest:
■Spacer -- Citadel: Old, Unhappy, Far-Off Things
■Earthborn -- Citadel: Old Friends
■Colonist -- Citadel: I Remember Me
■Shepard's choice to aid Sha'ira in Citadel: Asari Consort.
■Shepard's choice to aid Samesh Bhatia in Citadel: Homecoming.
If the body was released to Samesh, Shepard receives an e-mail from Samesh thanking Shepard for the help. There will also be a news story indicating that the Alliance is having difficulty in meeting recruiting quotas due to fears of 'superior' geth technology.
■Shepard's treatment of Conrad Verner in Citadel: The Fan
Shepard will run into him on Illium, but the interactions are identical regardless of prior treatment. This is due to a glitch in the first Mass Effect which activates both the "Charmed" and "Intimidated" flags, but forces the "Intimidated" option as the default.
■Shepard's choice to aid Emily Wong in Citadel: Reporter's Request.
■Shepard's choice to aid Chorban in Citadel: Scan the Keepers.
Chorban sends an e-mail about his scientific findings about the keepers; the text of the e-mail will vary depending on the number of keepers Shepard scanned in Mass Effect.
■Shepard's choices while being interviewed by reporter Khalisah Al-Jilani in Citadel: The Fourth Estate.
This quest occurs in Mass Effect 2 regardless of whether or not you completed it in Mass Effect. There is slightly different dialogue based on how Shepard interacted with the reporter in Mass Effect.
■Shepard's choice to help Dr. Chloe Michel in Citadel: Doctor Michel.
If the assignment was completed in Mass Effect, an email will be received in Mass Effect 2, in which Dr. Michel says that she is happy that Shepard is alive and hopes the Commander can visit her on the Citadel.
■Shepard's advice to Rebekah Petrovsky regarding her baby in Citadel: Family Matter.
Their conversation can be overheard in one of the shops on the Citadel, which differs depending on Shepard's advice. This conversation occurs in Mass Effect 2 without an imported save file.
■Shepard's interaction with Helena Blake in UNC: Hostile Takeover.
If Blake survived in Mass Effect, Shepard will run into her at Afterlife on Omega. The dialogue will vary depending on how Shepard resolved the mission.
■Shepard's interaction with Corporal Toombs in UNC: Dead Scientists.
■While Shepard's actions in UNC: Geth Incursions have no effect on Mass Effect 2, hacking geth data files during the mission is necessary to trigger Tali's personal quest, which does have an effect on Mass Effect 2.
■If the entire string of Cerberus quests (UNC: Missing Marines→UNC: Cerberus→UNC: Hades' Dogs) are completed, you can talk with Miranda about these activities, and will hear news reports about an investigation, which can involve additional testimony from UNC: Dead Scientists depending on how or whether you completed that assignment. Finishing every assignment will cause Garrus to question Shepard's choice to work with Cerberus, reminding Shepard about the experiments they had done.
■Shepard's decision in UNC: Hostage.
■Shepard's completion of UNC: Rogue VI.
This allows for additional dialogue options with EDI and Miranda regarding AIs.
■A news report will reference the events on UNC: Besieged Base, but due to a bug in the first game, the file is flagged as stating that the Sirta Foundation never recovered from the attack and will likely be shutting down.
■Shepard's decision to aid Nassana Dantius in UNC: Asari Diplomacy.
Nassana will recognize Shepard, and comment on the irony that Shepard has been "sent to kill her", referencing her sister's murder.
■Shepard's choices in Bring Down the Sky (DLC).
There will be different news reports depending on whether or not Shepard let Balak go to save the hostages. If Bring Down the Sky was not played, the news story indicates that the hostages died.