Simple
Once the arms are fully opened, the crucible fires a pulse throughout the galalxy that reprogramms the reapers to stop the harvest. After a moment, the reapers are seen leaving. It does not effect the geth or the edibot
Or it fires the red beam of goodies destroying all the reapers. Geth and the edibot are ok.
To determine which one really happens, BioWare will flip a coin. Heads for destroying the reapers. Tails for reprogramming the things.
The best part about this is it avoids the magic carpet ride up to lala land. It avoids the thing calling itself catalyst even though its creators call the thing, intelligence. It avoids you do not know them, and there's not enough time to explain comment. It avoids the synthesis is the final evolution of all life comment. It avoids the shoot this, pull this and jump in this endings.