Soyuz MS-09 was a Soyuz spaceflight which launched on 6 June 2018. It transported three members of the Expedition 56/57 crew to the International Space Station (ISS). MS-09 is the 138th flight of a Soyuz spacecraft. The crew consisted of a Russian commander, and an American and a German flight engineer. The mission ended at 05:02 UTC on 20 December 2018.

During the night of 29 August 2018, a small air leak in the ISS was noticed by ground control. A 2 mm hole in the orbital module was discovered, later stated to have been "hidden with a low-quality patch job." Russian crew members used Kapton tape to temporarily seal the leak while a permanent fix was devised. The leak was successfully sealed with the use of a repair kit based on an epoxy sealant, and no further changes in air pressure were noted as of 31 August. On 4 September 2018, it was announced that the hole was created by a drill, but it was unclear if it was accidental or deliberate. Russian officials indicated the hole was some kind of sabotage, perhaps during the module's manufacturing process. Russian officials even speculated that one of the NASA crew members had drilled the hole.

On 11 December 2018, Kononenko and Prokopyev conducted an EVA, cutting into the thermal blankets and pulling away insulation, in order to examine the external hull, take images of the area and retrieve samples of residue to be used in the investigation. As the hole is in the orbital module that is jettisoned before re-entry, the return flight was not endangered. The return of the MS-09 crew was briefly delayed by the launch failure of Soyuz MS-10 (until the arrival of the next crew on MS-11). MS-09 landed on 20 December at about 05:03 UTC.

Further reports and investigation were enacted thereafter. Prokopyev was quoted as saying that the drill hole was made from the inside; however, it is still unclear when it was made. In September 2019, the head of Roscosmos Dmitry Rogozin claimed that Roscosmos exactly knows what happened, but that the agency would keep this information secret.

Further reports and investigation were enacted thereafter. Prokopyev was quoted as saying that the drill hole was made from the inside; however, it is still unclear when it was made. In September 2019, the head of Roscosmos Dmitry Rogozin claimed that Roscosmos exactly knows what happened, but that the agency would keep this information secret. On April 20, 2021, a major Russian language tabloid Moskovskij Komsomolets published an article citing a post by Vadim Lukashevich in Facebook who claimed that the hole was drilled by Serena Auñón-Chancellor,which was disputed by NASA and called "preposterous" by Ars Technica

With a mission that was anything but mundane, Soyuz MS-09 with its three-person crew returned to Earth after more than 6 months in orbit on the International Space Station. The Soyuz MS-09 vehicle rose to high public profile in August when a hole that resulted in a small atmospheric leak aboard the Station was discovered in its Orbital Module.

That hole was determined to have been drilled on the ground during the spacecraft’s manufacturing and led to a rather dramatic spacewalk earlier in December that saw cosmonauts cut into the protective casing around MS-09’s Orbital Module to conduct further investigation of the issue.

Wrapping up its mission, Soyuz MS-09 and its three-person crew from Russia, ESA, and NASA, undocked from the International Space Station at 20:42 EST (01:42 UTC on Thursday, 20 December) before landing on the Kazakh steppe at around 00:03 EST (0503 UTC) on Thursday, 20 December.

Official confirmation that the hole was caused by a drill was announced on 4 September 2018, though it could not be determined whether the hole was drilled intentionally during manufacturing – aka, sabotage – or was the result of a manufacturing error.

Despite the admission, what was abundantly clear was that workers on the ground had identified the hole and sealed it in an attempt to cover it up, thus allowing Soyuz MS-09 to pass all pressurization and leak checks prior to launch.

The presence of the hole and its undocumented fix also raised serious concerns about the safety and quality control methods in place within Roscosmos in building the as-yet-still only vehicle capable of transporting crew to and from the International Space Station since the retirement of the Space Shuttle fleet in July 2011.

Perhaps serendipitously, the presence of the hole in Soyuz MS-09’s Orbital Module is arguably the best place the hole could have been since the Orbital Module does not survive atmospheric reentry.

In short, the fact that the hole is in the Orbital Module means that it poses no threat to the safe return of Alexander Gerst (ESA), Sergey Prokopyev (Roscosmos), and Serena Auñón-Chancellor (NASA).

However, the fact that the hole made it through safety and quality assurance checks before launch also raised serious questions of whether other holes exist throughout the Soyuz MS-09 vehicle – a question which cannot be answered with certainty until the craft returns to Earth.