After the main mission is done Kelly will send a message to your terminal. To make this happen you must have spoke the first time you met, then everytime you got a new member throughout the game and agreed with her in a flirty way. You also have to make sure that when the option comes to ask 'Are you into aliens?', the other thing you need to do is take her out for a meal, to do this talk to her after you recruit Samara and flirt with her.

The final thing you have to do is when you have finished the mission with Joker then go straight through the Omega 4 Relay and you will save her instead of seeing her die in the case on the last mission.

To get the message to come up after the game you must not be in a romance with anyone, for example, when you end a romance then the message will come up (it's basically waiting to pop up). This happens because you need to use the computer terminal in your cabin to call her down and if your already romanced with someone then it will have the option to call that person down instead. If you have followed all of these steps and it still doesn't show then head to a planet, come back and and go check your mail it should be there now.

Hope this helps, enjoy.