This subject probably has been discussed before at KingTutOne, but seeing as how I'm new here and wouldn't know where to direct you, Kiya, perhaps I can provide some help myself.
When the unremarkable Tuthmosis II died in around 1479 BCE, the crown prince Tuthmosis III Menkheperre was but a young boy and unable to rule on his own. The half-sister and wife of Tuthmosis II, Hatshepsut, stepped up as regent for her young nephew (Tuthmosis III was the son of Tuthmosis II by a minor wife named Aset).
The study of Hatshepsut is a lesson in political maneuvering; she was a strong-willed, shrewd, and intelligent woman. By about the seventh year of rule of the young Tuthmosis III, Hatshepsut set herself up as pharaoh and took on a full royal titularly. And she ruled as pharaoh for the next twenty-some years while Tuthmosis III languished in the background; interestingly, however, Tuthmosis III was also regarded as king at the same time, but it was Hatshepsut who truly held power. To accomplish this she most certainly had to have powerful allies among the high-ranking courtiers in the Egyptian government.
She also had enemies, or in the very least men who were openly suspicious of her role as pharaoh. Though there was precedent for a woman on the throne, it was never a desirable outcome. It ran counter to the core of Egyptian religo-politics. Make no mistake that ancient Egypt was a pure theocracy, bound by religious precepts to its core.
In this respect the royals were viewed somewhat as mirror images of the gods. Osiris was the first rightful king--a man--and Isis his loyal wife--a woman. Once Osiris was murdered, and after the Ennead ruled that Set had acted counter to maat and that Horus was the rightful heir, Horus, son of Osiris, then took the throne. We see here that the king is a man and his heir is a man, and that is the way of things.
So a woman on the throne made for unpleasant circumstances. Hence, Hatshepsut was known to have herself depicted as male in royal statuary and reliefs, to make her more acceptable. There's no evidence as of yet that any attempt ever took place to unseat her, but for certain she must have ruled with a heavy brow. Still, she did a marvelous job. Hatshepsut is one of my favorite pharaohs. She ruled a peaceful and prosperous Egypt and, in my humble opinion, left us one of the world's most remarkable architectural accomplishments in her mortuary temple at Deir el-Bahri.
And at her temple she left in its walls the story of her proudest accomplishment: the lucrative trading expedition to Punt. Among those reliefs is one of the most memorable figures ever carved, the rather "ample" queen of Punt
(note the figure second in from the right).
Hatshepsut died around 1458 BCE, and that's when Tuthmosis III Menkheperre finally assumed full control of the throne. We all know the story of Tuthmosis III, the great warrior king and conquerer of vast swaths of Lower Nubia and ancient Palestine.
Egyptologists have begun to rethink the defacing of the monuments and reliefs of Hatshepsut at the hands of her nephew, Tuthmosis III. It used to be the thought that he ordered their destruction immediately upon taking full control of the throne, as an act of vengeance for having been forced into the background for so many years even though he was rightful king and heir. But that's no longer the thought. It is now known that Hatshepsut's monuments were not defaced until many years after Tuthmosis III's full rise to power. He himself may not have had anything to do with it--it's possible courtiers ordered it done in his name. But it's also possible he felt compelled reluctantly to go ahead and order it, to restore the proper sense of maat to the throne for the sake of posterity. In other words, there's no real evidence to suggest that Tuthmosis III felt anything but affection for his aunt, even if she did keep him stashed away for so many years.
I hope this is of some help, Kiya. And I also hope I didn't bore you to tears. Sorry this got so long.
I just happen to be a big fan of Hatshepsut. Heck, the whole 18th Dynasty, for that matter.