In this game our main mission is to unite humanity and aliens of the galaxy in order to stop the reapers( godlike machines that come every 50000 years and wipe out all intelligent civilizations.)
In the last part we achieved peace between Geth(intelligent robots) and the quarians. We also killed a reaper and gave Geth a true intelligence(at the cost of our friend Legion's life).
This time we met with our former crewmate Zaeed. He was hired to kill a volus ambassador who was working for Cerberus(pro human terrorist group). Ambassador wanted to stop working for Cerberus but turians believed that he is still a traitor so they hired Zaeed. We saved the ambassador because he knew what colony Cerberus is gonna attack next. Volus ambassador did not wanted tell us this info and offered us a Volus bombing fleet. So we asked Zaeed to beat him up. After Volus ambassador told us the name of the colony that will be targeted by Cerberus AND gave us the fleet as well.
After that we met with asari councilor. She knew that we are missing a final peace for Protheans weapon that we are trying to build and destroy Reapers. She told us that we can likely find some answers at some asari temple at asari homeworld Thessia. So we traveled there and found out that Thessia is about to be destroyed by Reapers attack. We met with a group of asari led by Lieutenant Kurin who were still resisting the Reapers. They were planning to run away but our Prothean companion Javik was able to convince them to keep fighting and help us reach the temple. We defeated some reaper units on our way including two mechanical dragons know as harvasters. But the asari stood no chance and were just buying as time to get info from the temple.
We reached the temple and began looking for the artefact. We found out a few things. Beings who asari worshiped as gods were Protheans. And they were guiding and manipulating asari to prepare them for Reapers invasion. Also the artefact that we were looking for was a prothean beacon. Asari hid it from the rest of the galaxy and used it to advance their species. After that we activated the beacon. It turned to be a Prothean computer. It said that that we are doomed already. We told it to shut the hell up. After all we already beat some Reapers. Prothean VI was about to tell us the info we wanted. But at that point VI detected that a person indoctrinated by Reapers is nearby.
Indoctrinated person turned out to be Kai Leng. The best agent of Cerberus who killed our friend Thane. At first it seemed like he has no intention of fighting us. That he was just there to give us a phone hologram call from Illusive Man(leader of Cerberus). Illusive Man started babbling about how we should not destroy the Reapers but control them instead. We told him that we will do this our way(destroy the Reapers). After that we fought with that bastard Kai Leng. We were beating the hell out of him but then he beat us in a cutscene. After that he got the info from the prothean VI and escaped. Soon after that Thessia was completly lost to Reapers and we barely escaped.
Our specialist Traynor was able to track Kai Leng ship close to a place called Sanctuary. It was believed that Sanctuary is a safe haven for war refugees. Also that coward Kai Leng had the nerve to write us an email mocking us. In the future we will go after Kai Leng but first we will do another DLC.