This sounds like it might be the unproduced film script Shadow 19, by screenwriter Jon Spaihts.
The protagonist, Captain Conrad Vance of the Offworld Marine Corps, is ordered to serve as the subject of a research project, located deep underground, which is run by the "Science Agency" and kept secret even from the government:
ELEVATOR: [...] Lights flash to life, and the elevator descends.
The floor indicator reaches the lowest basement level - but the elevator KEEPS SINKING.
[...]
SECRETARY DAIN: The Department of Defense relies on the State Science Agency for key technologies. When they requested a Marine for special duty, I couldn’t easily say no. I’m beginning to regret that decision. I want to know what this project's about.
VANCE: I signed a writ of secrecy, sir. I can't say much.
Vance is informed that his new, top-secret mission is to travel to the planet Erix by means of the instantaneous "Lang Transporter", make a hazardous multi-day trek from the transporter to an an unmanned crawler, and repair it. The crawler is supposed to be taking part in an autonomous terraforming operation, but has been damaged by the unexpectedly ferocious native lifeforms, which have evolved to take advantage of the planet's high metal content:
ADA: Erix is richer in heavy elements than Earth. Tungsten, chromium, titanium. Living things on Erix incorporate those metals.
From Vance's point of view, the teleportation process initially appears to fail:
The transport chamber’s door opens. Vance steps out onto the catwalk. He’s untouched, his armor unmarked.
VANCE: I’m still here.
DIRECTOR MARBECK (O.S.): Technical difficulties, Captain.
[...]
VANCE: Technical difficulties. But this is safe.
DIRECTOR MARBECK: Perfectly safe in theory. It takes a week to recharge the transporter. One week. Until then - continue training.
but unbeknownst to him, a "shadow" duplicate of him was successfully sent to Erix, and then promptly killed by alien wildlife.
After a few more "failed" teleportation attempts, he starts getting suspicious and presses the scientists for an explanation, and the scientists reluctantly explain the true nature of the teleportation process. From that point on, Vance involves himself in the planning of subsequent iterations, using increasingly powerful armor and weapons. Eventually:
his 19th "shadow" is successful in reaching and repairing the crawler. However, both the original Vance and Shadow Nineteen find evidence that the terraforming project is in the process of exterminating a native race of sentient beings, which the Science Agency knew about and covered up.
Shadow Nineteen sabotages the project, rides the crawler back to the transporter, and hotwires it to teleport himself back to Earth. The resulting duplicate of Shadow Nineteen teams up with the original Vance, and they (plus Vance's romantic interest, a rebel scientist) have to fight their way out of the research station, in order to reveal the truth about what the project has been up to.
