When you enter the Shroud, Mordin will prepare the cure and begin the upload. He will quickly discover the inconsistencies with the Shroud’s temperature, as Dalatrass predicted, and move to fix it. He will have to head to the top of the tower, which will be bathed in explosions and gunfire from the Reapers, in order to correct the temperature and save the cure. At this point, you can choose to either delay Mordin for Renegade points, or allow him to go up unhindered for Paragon points.
Beware, BIG SPOILERS FOLLOW!
If you choose to allow Modrin to proceed to the top of the Shroud, this process will be relatively painless. He will get into the elevator, Shepard will wish him luck and leave the erupting facility, and Mordin will successfully process the genophage cure through the Shroud. However, he will do so at the cost of his own life. The facility will explode around him after the cure has been distributed through the air.
If you choose to delay Mordin, he will see right through your act and confront you. In this confrontation, there are several possible results. First, if Wrex survived the first Mass Effect and is currently leading the krogan troops outside, Mordin will refuse to deny his friend the genophage cure. He must atone for his past sins in infantilizing the entire species, or so he feels. This will leave you with two options. One, you can allow Mordin to proceed to the top of the tower unopposed, which will lead to the previously mentioned outcome of his distributing the genophage before dying. The second option is to kill Mordin yourself, thus denying the krogan the cure to the genophage and securing the allegiance of Dalatrass and her salarians. Keep in mind, however, that if you do allow Mordin to proceed with the cure, you will not lose all of the salarians, merely the ones under Dalatrass’ command. When you return to the Normandy after this mission, you can speak with Admiral Hackett to learn that several splinter factions of salarian troopers have left their home planet behind and joined you in your fight against the Reapers. It’s not as significant as having the backing of their entire species, but it’s something.
However, if Wreav is the krogan leader and you did not pursue Maelon’s research in Mass Effect 2, then Eve will be dead and Wreav will be leading the krogan with a barbaric hand. Then, and only then, you can actually convince Mordin to allow the cure to fail. You can also proceed with the previous two options of allowing him to go up or murdering him. If, however, Eve is still alive, you will not be able to convince Mordin to leave his research to die even if Wreav is the leader of the krogan.
If you sabotage the genophage, the Dalatrass will be true to her word and you will gain the allegiance of both the entire salarian species as well as the entire krogan species. But if Wrex was alive and you had to murder Mordin to secure this tenuous alliance, be aware that not all will remain smooth sailing. While Wreav will be too dumb to discover your treachery, Wrex is cunning, and will eventually find out that you double crossed him. Blinded by rage, he will threaten to reveal your treachery to his entire species, or worse, kill you on the spot. You will have no choice but to kill him, and in doing so, sacrifice the allegiance of his entire species, as you essentially have just murdered their King.
Following the decision in the Shroud, either the cure or the fake cure will spread from the Shroud, forming a large cloud over Tuchanka. Snow will begin to fall, and the krogan will rejoice, as their cure has finally arrived (or so they will think, if you sabotaged the cure.) If Eve died, you will see a scene in which the krogan give her a warrior’s funeral. Otherwise, she will be present outside of the Shroud, and will thank you for all of your hard work towards her cause.
Despite Mordin’s sacrifice, Wreav will claim that history can never tell that the salarians cured the genophage, after they were the ones who created it in the first place. You will return to the Normandy, where a conversation with Admiral Hackett will take place. During this conversation you will learn that the krogan were true to their word and rushed to help the turians on their homeworld of Palaven. With the help of the krogan, the turians were able to successfully turn the tide of the battle and save what little was left of their planet. Although the Reapers still launch attacks against Palaven, it will soon be safe enough for the turians to send their forces to support Earth. You can also inquire about the standing of the other races in the galaxy. Here you will learn of the plight of the asari, whose home planet is currently facing annihilation from the Reapers. This will be your next stop, although you will have to stop by the Citadel first to report your success to the Council.
After talking to Hackett, Shepard will retreat to his/her quarters. This will trigger another dream sequence. Simply follow the child as he leads you through the ashen landscape. The voices of your dead crew and friends, if you have any, will ring through your ears as you follow the child. A similarly gruesome ending will await him at the end of the dream. When you wake, Liara will come in to check on you. You can either admit your bad dreams to her for Paragon points and a closer relationship, or deny them to keep her at bay. If you admit your bad dreams to Liara, she will ask specifically who you were dreaming of. Respond that you were dreaming of Ashley or Kaiden, and the two of you will briefly reminisce about your fallen squad-mate. Liara will tell you that you have a message on the vid-com, so head there after you finish your conversation. Dalatrass will express either disappointment or delight in your actions. From here, you will be free to roam the Normandy before taking on your next missions.