In this part we arrived on a planet Virmire. We had to help infiltration team of salarians who were investigating the area. Leader of salarians captain Kirrahe told us that Saren's base is on Virmire. And appearently Saren found a cure for genophage and started breeding an army of krogan. After that we had an argument with Wrex. He wanted to keep the cure while Guts Shepard believed that Saren's facility and the cure for genophage has to be destroyed. Luckily we did Wrex side quest and found his family armor. This allowed us to calm him down and convince to do things our way. Wrex and Garrus are like bros for Shepard so it is great that Wrex survived our argument. After that captain Kirrahe asked to sent either Ashley or Kaiden with salarians. We chose to send Ashley. After that salarians attacked Saren's base as a distraction. At the same time Guts Shepard and his remaining crew were attacking as the main force. Inside the base we found something we did not expect. It turns out that this base was not just for breeding krogans but also to investigate the effects of indoctrination(brainwashing done by Saren's ship). In Saren's personal quarters we found another Beacon similar to the one we found on Eden Prime. It gave us the same vision we had before. But this time it was a bit more clear. We were about to leave Saren's personal quarters but then a hologram of the ship appeared. Then we found out the truth. It was not a ship it was an actual Reaper whose name was Sovereign. One of many giant machines who come every fifty thousand years and destroy all advanced civilizations. After that Kaiden set up a bomb that had to destroy Saren's base. Then Ashley called and said that she and salarian team are in danger. So we went to save them. We did not get far because Kaiden informed us that he is also under attack. We could save either Ashley or Kaiden. So we went to save Ashley and salarians. There we encountered Saren and found out that he is also already indoctrinated by Sovereign. We fought but Saren escaped. After that we flew away with the Normandy as well. Kaiden sacrificed himself while making sure that bomb goes off and destroys Saren base.
Ashley wanted to know why we chose to save her and not Kaiden. She blamed herself for his death. Liara came up with an idea of joining our minds again to make sense of the vision we got from Beacon. This time it helped...a bit. Liara figurauted that Conduit( the thing Saren is looking for) is on Ilos planet. The problem is that we can only get to Ilos using Mu Relay and we still don't know there Mu Relay is. After that we spoke with the Council. Crazy bastards still did not believe our warning about the Sovereign and the Reapers. So we disconnected their call again. After that we spoke with our crew again. Garrus thanked Guts Shepard for taking him with us. Wrex had calmed down and now respected our choice to destroy Saren's base. Ashley was worried about our chances of victory against enemy as powerful as the reapers.