To have encounters with Alex, first complete the Portal Panties questline. After, go back to the engineer and ask him the non-purchase dialouge questions. At a certain point there is the option to ask to help him. He will intially decline but allow you to watch his work. Do this for a couple days until he opens up about furthering your relationship. Complete the submission questlines and on eventually he will gain enough trust to engage you in his last 'lessons'.
Another method is to duplicate a static NPC and enslave them using the Debug menu. It should do what it says on the tin and I think it doesn't have a limit on how many times you can do that, just be careful not to crash anything by messing with the variables.
There is also an Alex mod which extends his storyline a bit although it may not be up to date with the current version.