Thutmose III's mummy was discovered in the Deir el-Bahri Cache in 1881 along with several other eighteenth and nineteenth dynasty leaders. Overall, his mummy was not in good shape because it had been damaged by tomb robbers.
It was originally thought that Thutmose III’s mummy was unwrapped by Gaston Maspero in 1886, however it was revealed that it was first unwrapped by Émile Brugsch who supervised the evacuation of the mummies from the tomb in 1881. This was while Maspero was away in France, so the Director General of the Egyptian Antiquities Service arranged for the mummy to be re-wrapped. As a result, when the mummy was unwrapped by Maspero in 1886, it was in a moderately poor condition.
The cause of death of Thutmose III is unknown. He died during his 54th regnal year.
Thutmose III: The Napoleon of Ancient Egypt. (2015). Retrieved December 3, 2015, from http://discoveringegypt.com/ancient-egyptian-kings-queens/thutmose-iii-the-napoleon-of-ancient-egypt/
Thutmose III. (n.d.). Retrieved December 3, 2015, from http://www.ancient-egypt-online.com/thutmose-III.html
Drower, M. (2014). Thutmose III: King of Egypt. Retrieved December 3, 2015, from http://www.britannica.com/biography/Thutmose-III