You'll meet them in a space area for a meeting. This is the dividing factor as it's worth mentioning that Dalatrass Linron is hostile to the genophage cure and the krogans. So it's simply being on the side of the krogan or sacrificing the krogan for the salarians but the surprise decision would come later.
Meet EDI[edit]
If you haven't done so, go to the doctor area and go in. The fire and smoke ended and it turns out that EDI is in Dr Eve's body. Of course of the affection from Joker, it's revealed that he removed the shackles that allows EDI to have her own free will. To know more about EDI, she's basically a robotic computer and can be quite hard to get the grasp because she's gathering data but she's also now your squad mate.
Saving the female krogan[edit]
This level is straight forward. For more details, assuming you have Wrex coming along to the science centre. A quick backstory, if you save Wrex, he'll be more gung ho in seeing through the alliance. But if you have killed Wrex, Wreav instead will take his place with a more tame approach. The same goes with Mordin. If Mordin has died in a suicide mission, Padok Wiks takes over his role.
Checkpoint by checkpoint[edit]
Once you're done with your conversations, go to the elevator with a bomb?! Oops! So go on the other side and up the ladder. Your job throughout this is once you reach the place with the console and the female krogan inside, press the button to continue as there is about five levels. Each has Cerberus troops and shield wielders with the Cerberus Atlus at the end. Of course, the female krogan gets to shoot the last two troops. The final conversation regards the failing health of the female krogan now called "Eve".
The next missions will be explained by Primarch Victus and Wrex/Wreav.
Spider's Web[edit]
If you have spoken to Wrex/Wreav, go to the location to start your next mission. Grunt or Dagg is heading the Aralahk Company. Check for weapons and mods along the way at the start. That includes weapon modification wear the krogan group stand, on the left side. Go on the right side and the compartments came crashing down! Anyway, you'll get early on the fire gun which you will use until the end of the mission. The key points is to take down webs, pods and to get across the Reaper barrier, fire on the node to unlock the barrier. Once you reach the giant cave, you got a choice depending on who's there. If the rachni queen lives, you can save her or punish her. Which ever choice you make, Dagg wouldn't survive but Grunt would.
Turian survivors[edit]
Once you spoken to Primarch Victus, go to the planet for a rescue operation. Your advantage is a surprise attack while the Reaper forces were busy with the turian soldiers. If you come across each escape pod, a harvester comes down to destroy it, so get yourself and your squad to take it down as quick as you can. Otherwise, the harvester would fly off as it counts into your experience. Do the same along the way until you reach Lieutenant Victus.
Note: Both these missions are optional with the third at the bottom. If you want raise more assets, it's ideal to do all missions to get the best outcome.
Turian bomb meltdown[edit]
You have to traverse through the war area taking down enemies. It's a walking, shooting journey as you realize along the way that Cerberus is evacuating. Anyway, once you reach Lieutenant Victus, Primarch's son, you have to protect him as the remaining Cerberus team tries to attack him once more, including the metal Atlus. The cutscene reveals the final sacrifice of Lieutenant Victus as he takes the trigger off the bomb.
If you do not complete this mission, later on you will watch this planet explode.
Genophage cure or not?[edit]
This will start with the intro of Shepard planning to distract the Reaper with turian air force and krogan ground troops. Before Shepard leaves, the Dalatrass Linron gives you another option that years ago, the salarians sabotage the genophage cure. You can reveal the sabotage or let them "believe" the genophage cure is safe. The key points is going through the Ancient Ruins, go across bridges and go through the stone sanctuary. After another conversation, you have to make across the Reaper attack safely, followed by the Brute army ambush as you have to set the hammer's on to get the Kalros to take down the Reaper. The last part runs in two ways, you let Mordin/Padok Wiks save the cure or kill them. Also, Wrex has a rival Wreav that's killed by Kalros. Alternatively, if Wreav's the leader, than Virmire gets killed by Kalros.
As a default for the whole thing, especially the Wii U version, Maelon's care failed resulting in Eve's health detoriating to her death which you will see at the end. Only on the PC, PS3 and Xbox360 can you change that, allowing Eve to live instead.
Once it's over, you'll go through another dream sequence with the kid. Finish the remaining missions if you want before heading back to the Citadel.
Warning: Make sure before you go on a Genophage Cure mission, to complete all available sidequests because after the attack on Citadel, certain sidequests won't be available as new ones will be replaced.