The element known as Phlogistone is a powerful source of renewable clean energy created from the reaction of the Moon's ore with numerous different types of energies, including cosmic radiation, M'Kraan Crystal energies, Phoenix Force radiation, the Beyonder's energy, Infinity Gem manifestation, and the White Event.
Not long after the White Event, the Phlogistone started manifesting in the surface of the Moon. The robot Udarnik found it and discovered it was a powerful source of energy, with which he created his Lunar fortress, the "Crimson Dynamo." With the Phlogistone, Udarnik empowered weaponry he used to attack the Earth in order to draw the attention of humanity.
When Iron Man investigated the attacks coming from Earth's satellite, he met Udarnik, with who he came to terms after being attacked. Udarnik showed Stark the power of the Phlogistone, at the same time he broadcasted to Earth the existence of this powerful material. Humanity returned to the Moon and created a colony, from which investigations about Phlogistone and plans for extracting it begun.
Tony Stark, who had become the governor of the Moon, discovered that prolongued exposure to Phlogistone caused degenerative effects to the brain, including megalomania, obsession, psychosis, hallucinations, and eventually death.
Following this discovery, Stark planned to stop this material from reaching Earth by destroying it, for which he acquired the maps of all the Phlogistone deposits from Cortex Inc., one of the main mayor players in the search for this material, by breaking into their databank, a process which also helped him to plant evidence against Eli Warren, another contender for Phlogistone, to make him be kicked out of the Moon, possibly having actually succumbed to the obsession for Phlogistone and megalomaniac tendencies caused by the exposure to it.
From the Doctor Doom of an alternate future who arrived to the present in order to empower himself with Phlogistone, Stark acquired a device which allowed to extract the Phlogistone's energies (which poisoned the brain) and render it simple iron. Before Stark could add the device to his armor in order to render the Phlogistone which was poisoning him inert, Udarnik captured him, as he had discovered Stark's plans to render Phlogistone useless.
Tony escaped captivity and reached the device, but he was intercepted by Udarnik. Stark managed to convince Udarnik he had to render the Phlogistone inert, but just in case, he heavily damaged Udarnik's body to prevent any interference. Stark powered up the device, cleaning his blood in the process, and redirected all of the Phlogstione's cosmic energies which composed it to space, leaving all of the Phlogistone transformed into simple iron.
Phlogistone is likely named after phlogiston, a chemical that was once believed to have been released during combustion prior to the discovery of oxygen. Its existence was eventually debunked by Antoine-Laurent Lavoisier. The name may also come from phlogiston's origin word "phlogistós," Greek for inflammable, in reference to Phlogistone's flaming red appearance.