The next mission will lock you into the endgame. Do it only when you're ready to finish the game. Do Leviathan and Citadel now, and make double sure all loose ends are wrapped up before triggering the mission.
Man, Kai Leng is an utter blight on a fantastic Thessia mission. The whole atmosphere and tension is great running up to the temple as you legitimately feel like the entire planet is falling with one last gasp to save the galaxy, then that guy shows up in three feet in plot armor accompanied by a massive gunship. Then the cutscenes make everyone ineffective so the creator's pet can shine, with that hilarious email as the cherry on top.
For the record I like having Shepard fail here, but there are much better ways of doing it and having Cerebrus win than what happened on the mission.
P.S. On "The legend of Shepard needs to be re-written. I hope I'm there for the last chapter. It ends with your death," the last line is like "The hammer is my penis" from Dr. Horrible's Sing Along Blog if the whole production was done completely straight-faced.
There is something with Zaeed, check Shepard's email. One of them should be from Primarch Victus asking Shepard to investigate a situation on the Citadel involving a Volus, and you can follow up on that at the Specter office terminal (where you can authorize things). If that's already been done, try going to the office to the left when you got off the elevator to the Embassy where the quest picks up.
Alex has a few quests ongoing to pick back up, like the code he found in the hospital that he should do. I'd look up a guide or the Mass Effect wiki for the steps, Mass Effect 3's journal doesn't show steps in a quest. While clearing things up have Alex open the map, it automatically shows people he can talk to for dropping things off, or Normandy crew (including squad members) on the Citadel.
You can do Leviathan or Citadel anytime before the point of no return. For reference, that should after the next two Priority missions (not including speaking with the Asari councilor.
@awkwardl0ser: If you romance him in Mass Effect 2 he leaves you without saying anything while you're under arrest, cheats on you, and gets the leader of the group you meet in his mission pregnant.
Your Shepard's mom is alive due to the Spacer background you picked, you can talk to her in a side mission you missed in Mass Effect One. Don't know if she knows up as a war asset. Otherwise, Shepard's parents are dead in the backgrounds.
Tali unmasked appears as a picture if male Shepard romanced her, but it's an altered stock photo if I remember correctly.
Vinny,
Encourage Alex to bring Javik on the main story mission. It will be the mission that requires Liara to be part of your squad, and Javik has a massive amount of unique dialog throughout the mission.
When Alex does the mission to save Admiral Koris, encourage him to make sure he saves the admiral on the mission, or it'll make the final choice of the arc impossible.
Going into systems and scanning lets you find assets to use in the war, like the Pillars of Strength this episode. It can also find you more money, fuel, or other items to become war assets and increase your numbers. I'd go through the systems at least once to round up everything, the game will show a percentage for each area once you've found something in that area. If nothing comes up, scan all the planets in that area. If you find nothing there, then the system currently has nothing to find.
When you find something like the Pillars of Strength by scanning a planet or on a mission, the map will indicate who you can turn something into like the "Asari Scientist" listed on the Hospital map this episode. None of this is time sensitive, but will improve Alex's war asset numbers so get them done.
But do pick up everything you can and drop them off before doing the Shroud mission, things will be locked out on the Citadel after you visit the Shroud.
Have Alex go to the Citadel to get his fish back, find Kelly Chambers on the station. She's listed on the map, but should be in the holding area. While you're there, make sure he checks all the shops, one should have a Fish VI for sale that automatically feeds his fish.
Zandrake94's comments