As you should now realise after the mention of Cyclops and Archangel, sometimes the greatest threats to the X-Men come from within. When Jean Grey was transformed into the Dark Phoenix, she nearly brought an end to everything they stand for, and while imbued with the awesome power of the Phoenix, went as far as destroying entire planets. It was only when Jean regained control and sacrificed her life that she was stopped. Jean later returned with power over that entity, but following her death (this time at the hands of Magneto imposter, Xorn), she's remained gone. The Phoenix Force however has not, and caused a lot of problems for the X-Men when it made its presence felt in the Avengers Vs. X-Men storyline, imbuing other members of the X-Men with its power and driving them mad in the process, something which fractured the mutant race.