The genophage has been a major point of focus in the Mass Effect franchise from the start. Designed by the Salarians to slow Krogan population growth and keep their violence in check, the genophage all but destroyed the Krogan and prevented them from evolving beyond the brutish, battle-hungry warriors that could have dominated the galaxy if left unchecked. With the Reapers threatening to decimate the Turian homeworld, Palaven, the Turians can only offer aid to Earth after their own problem has been dealt with.
Primarch Victus wants Krogan aid for Palaven, but the Krogan will only help if all their people have been given the genophage cure. Distributing the cure means getting the Salarian scientist and the only Krogan female immune to the genophage to the Shroud tower, but it won't be easy. A massive Reaper is looming over the shroud, and Commander Shepard will have to get up close and personal with it to clear the way.
Mission: Protect Eve
On the way to the shroud to distribute the cure, there is a cutscene revealing that the Reapers are using the shroud to poison Tuchanka's atmosphere, and the Reaper presence means they won't be able to land directly at the site. They'll take a convoy to make sure the Krogan female, Eve, stays safe. Before leaving the Normandy, however, Shepard gets an incoming meeting with the Salarian Dalatrass, who reveals that the shroud was sabotaged years earlier to prevent anyone from doing what they are about to do. They offer a deal: Salarian scientists and military in exchange for not distributing the cure and letting the Krogan think they did. Shepard need not decide how to handle this just yet, but it is something to consider.
After taking a shuttle to the ground with Eve, the Salarian scientist (Mordin Solus if he survived Mass Effect 2's suicide mission; otherwise, it will be Padok Wiks) and the Urdnot clan chief (Wrex or Wreav if Wrex is dead) are to meet the rest of the gathering Krogan at the Hollows, an ancient meeting grounds. Shepard has an opportunity to reveal the Dalatrass's proposition, but before they can speak, their arrival at the Hollows reveals the place swarming with husks that need to be taken out before the meeting can begin. After wiping out the husks, there is a cutscene in which Wrex/Wreav argues with his biggest rival and Eve intervenes to remind them their behavior will no longer serve the Krogan race, especially once the genophage has been cured. She encourages all the present Krogan to unite instead against the reapers and the convoy to the Shroud resumes.
Mission: The Krogan Convoy
Upon rolling out, Eve will ask Shepard what they will say before arriving at the Hollows. Shepard can choose to reveal their conversation with the Dalatrass or keep it secret. Revealing it will allow Mordin/Padok to prepare a workaround for the sabotage at the Shroud, though keeping quiet about it does not yet mean Shepard won't cure the genophage. Shortly after this conversation, the convoy stops. The road is blocked, and they need to find another way to the Shroud. There is a lot of loot in this area to pick up, including a Shotgun Smart Choke upgrade, Pistol Magazine upgrade, Pistol Melee Stunner, a Death Mask Helmet, the Graal Spike Thrower Shotgun and two med-kits.
There are also a couple of conversation options with Krogan standing here before the Turian Air Strike team flies overhead, too close to turn back from the Reaper while the convoy finds another route. One of the ships is shot down and crashes into a convoy truck. Shepard radios to Wrex/Wreav and tells them to get out with Eve. They'll find another way through the ruins across the small chasm.
Leap over and head down the stairs into the ruins of an ancient Krogan city that has been abandoned for thousands of years. Either jump across the gap on the left or continue down the next set of stairs and turn right. There is a door on the left and on the other side is the first of three Ancient Krogan Artifacts, each worth 8500 credits. Scan the artifact and head back through the door to go down the stairs. The ground tremors periodically while in the ruins, which Eve will confirm is likely Kalros, the mother of all thresher maws. Drop down the ledge and turn left, heading to the far end of this area for another Krogan Artifact to salvage for 8250 credits. On the other side of the room, turn left into another tunnel where another artifact can be salvaged for 8250 credits before advancing and coming face to face with a strange corpse. If the missing Krogan scouts on Utukku were already investigated, Shepard will recognize this as a Ravager, the Reaper-corrupted Rachni.
Head up the tunnel and out of the catacombs into the aboveground area of the ruins. Travel forward and battle through the Cannibals and Ravagers in this area. Once clear, move forward and across the gap to face a wave of Cannibals and a Brute. This fight consists of two waves, during which Wrex/Wreav and Mordin/Padok will tease Shepard about taking too long. Once the fight ends, advance and turn around the bend just as a third wave attacks. Once they are dispatched, head toward the bridge on the right just as Kalros makes her first appearance. Approach the bridge to provoke another fight with husks and Cannibals, followed by more husks and a couple of Marauders. After killing them, pick up the SMG Scope and head into the area where the Marauders emerged. Grab the Assault Rifle Extended Barrel and then turn right to drop down a series of ledges to meet up with the convoy again.
Mission: The Maw Hammers
The Krogan have a crazy plan to summon Kalros to distract the Reaper so that Mordin can administer the cure. Shepard needs to strike the two maw hammers, one each on both the left and right of the area with a live Reaper in the middle. The Urdnot Clan leader will raise the hammers while Shepard navigates the dangerous area ahead to strike them. Head up the stairs and pick up with M-5 Phalanx Heavy Pistol and proceed across the bridge. The Reaper will blast the bridge, crumbling it so Shepard is on the ground. Shepard becomes its most immediate threat, so the Reaper will continue firing on them, so take cover and stay down until reaching the area where the hammers are located.
There are multiple Brutes in this area that need to be taken care of, on top of massive Reaper claws clamping down to block Shepard's path. If Shepard's squad can keep the Brutes busy, however, they can be avoided entirely by dashing toward the hammer and activating it, then rushing across to do the same on the other side. Once the hammers have been activated, it activates a cutscene in which Kalros comes and takes out the Reaper, dragging it underground and killing it. Now, Shepard has to decide how to deal with the genophage.
Mission: Cure the Genophage (or Not)
With the Reaper threat dispatched, Shepard and Mordin/Padok can focus on the shroud and the cure. If Maelon's data was not kept, Eve will not survive the Reaper fight and the genophage cure will not work. Even with Maelon's data, Shepard can still take the Dalatrass's deal and betray the Krogan if that is their choice.
Inside the shroud, Shepard can inform Mordin/Padok about the deal if they haven't already and kill him before they can fix the shroud, convince him to walk away if Wrex/Eve are dead or allow him to fix the sabotage. If Mordin walks away, he becomes a War Asset working on the crucible, but Padok leaves to live out the rest of his days on a remote world, promising to take the secret to his grave. If he was warned about the sabotage prior, he will fix it and distribute the cure but sacrifice his life to do so. Shepard can use the Paragon interrupt to try and stop him, but he knows he has to do it. Mordin/Padok cannot be saved if the genophage is cured, no matter what Shepard does.
It is important to note if playing the Renegade path that not curing the genophage can significantly decrease Shepard's overall War Assets if Wrex is the Urdnot Clan leader.