She never comes on the Normandy. As long you've:
- Met her on the Citadel(Normandy Docking Bay: D24)and rekindled your relationship during the Genophage arc.
- Read Kai Leng's Dossier from your message terminal prior to meeting Miranda again(Citadel Embassies(Spectre Office)). Kai Leng's dossier will be given to you after the Cerberus coup on the Citadel.
- Met with her for the third time(Citadel Presidium(Apartments in the left hall))and allowed her access to Alliance resources(also, do allow sexy time to lock-in the relationship). This must be done before heading to Thessia.
- Saved her and Oriana on Sanctuary with a Charm(Paragon option)or an Intimidation(Renegade option)during the conflict with Miranda's father(If you don't have enough Reputation I think you can still save Miranda if you shoot Oriana in the leg with the Renegade interrupt. If you don't press the renegade interrupt, Miranda will die).
Doing all of this should ensure her survival and your romance with her. Just make sure to check your private terminal often.