Very few people are privileged with the knowledge that an Infinity Stone is inside the Tesseract. It is mostly known as a source of near-limitless clean energy and a useful tool for creating Boomtubes. Unlike artificially created warp streams, there is no limit to the mass or reach of the Tesseract's portals and no trace neutrino emissions. The scale of what the stone can move is limited only by the willpower and focus of the user. A strong enough mind could potentially relocate an entire planet-- but very few beings in creation are capable of channeling such cosmic energy without being destroyed by it.
The Infinity Stone inside the Tesseract came to Earth with a Oan science expedition, and helped create the stable matrix around the Cosmic Cube. It was lost during the fight for the science ship, the Omrut Beacon.
Later it was recovered by mages of Atlantis, who created a stablizing matrix to regulate the Infinity Stone and prevent others from finding it. Merlyn entrusted it to Asgard, who kept it for generations in their deepest vaults. When Surtr threatened Asgard in the most recent Ragnarok Cycle, King Thor brought it to Norway and entrusted it with the priests of the Allfather.
It was stolen from Norway by the Harbingers during World War II. After an assault on a research facility by Allied forces it was recovered by the OSS. When SHIELD was formed it was designated as a 084 and set aside for research and study.
After several incidents resulting in alien incursions and uncontrolled energy detonations, the Tesseract was removed from the science labs and placed into secure long-term storage several decades ago. Its precise location is known only to a handful of the highest-ranking SHIELD officers.
Currently the Tesseract is in SHIELD custody.