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My story calls for the main characters to break up for at least two years, before getting back together. (In this particular case, the breakup is for ethical reasons - the relationship began when the two were therapist and patient)
How do I keep them apart but still keep the story going?
She is audited by the ethics arm of the board which gave her her professional license. He's a former patient. The board tells her to break it off or lose her license. In the intervening two years, she realizes that he is worth losing her license for, or alternately finds another job.
If you're writing in the first person, you can just continue with the story of the MC and what happens with his/her life during that time.
If you're writing in the third person, you can try to combine both stories during the time. Is he still the therapist during the two years and they "only" break the relationship or do they stop the therapy too? If they stop completely, you can just write their lives separated, each time one chapter or mixing the threads in the same one and divide chapters by "real-story" time.
They could each join the same social group, on accident (one character is already a member; the other then joins, not knowing). This would force them into proximity, which would generate conflict and tension dependant upon their initial split. You could ride this tension for a full two years, or introduce it later on -- a year in, or six months -- so that it could catalyze their eventual reunion, with a resolution or "snapping" of that tension.
If not: there's always pining, nostalgic longing, looking melancholically at pictures. Etc.
Good luck!
