I do a lot of cooking and storing on the weekend - roast a big pan of chopped veggies, roast beets separately in foil, saute spinach and mushrooms, caramelize onions, and poach a bunch of 5 minute eggs using 
poach pods.  Everything is stored in its own 
container.
I make a layered breakfast each morning in a microwavable container with a vent in the lid: 1/2 c. diced beets, 1/2 c. roasted veggies, a heaping spoonful or two of the spinach/mushrooms, and a spoonful of the onions.  Then I make a little cavity for the egg, and plop it carefully.  The onions will hold it in place fairly well.  I take it out of the fridge about 30 minutes before I plan to eat.  Microwaved about 3:30 minutes at 50% power, everything heats up without cooking - including the egg.  The white is done and the yolk is runny (my preference, YMMV).  All of it totally yummy.
The roasted veggies vary by season.  The combo right now is sweet potato, butternut squash, celery root, and red bell peppers.