Sometime after the events of Avengers vs. X-Men and the Inversion; Cyclops found a Phoenix Egg, and waited for it to hatch, hoping to use its power to stop the incursions. The egg did not hatch in time, however, only becoming ready during the final incursion. Cyclops hatched it, and bonded with the Phoenix Force once more.
Under unknown circumstances, Terrax the Tamer acquired a Phoenix Egg and stored it on his warship. Thane eventually learned about this, and deceived his allies (Champion; Starfox, and Nebula) into helping him invade Terrax's warship to steal the egg.
Alternate Reality Versions
Mapmakers Invaded Tian (Earth-2319)
Here Comes Tomorrow (Earth-15104)
A Phoenix Egg was recovered by Brian and Smith of the Proud People. It was taken to the X-Men by one of their number but the Crawlers stole it for their master. The Beast later incubated it through heat vision to give birth to the Phoenix.