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This article is about the ONI agent. For other Halo characters named "John", see here.
The Mona Lisa
In October 2552, Smith and his ONI science team took control of the prison vessel Mona Lisa with the intent of using it as a laboratory to study the alien parasite known as the Flood, in the hope of turning them into obedient warriors for the UNSC. Once aboard, they would jump into the Soell system, the site of the wreckage of Installation 04. There, they managed to capture specimens of the Flood and brought them aboard the ship.
Smith would then use both human and Sangheili prisoners to study the effects of the Flood. Whether ONI approved of his research is unknown; it was later noted by the ONI AI Rebecca that he had exceeded his original parameters "significantly", but this may also have been a result of Section III covering their tracks by putting the blame solely on Smith.
When the Flood eventually broke free and overran the Mona Lisa, Smith remotely launched most of the ship's escape pods to prevent the Flood from getting off the ship. According to Smith, he would also attempt to sabotage the bridge, but could not get close enough. He then retreated into the safety of a sealed panic room, remaining there until he was discovered by Sergeant Zhao Heng Lopez's squad. Smith, claiming to be the Mona Lisa's medical officer, began to insist that they should leave the ship immediately, but Lopez would ignore his pleas, as they were on a mission to clear the ship's navigation database in accordance with the Cole Protocol.
Upon coming across a Flood growth, Lopez inquired Smith as to its nature. Smith claimed that the Flood was a Covenant virus that had unexpectedly jumped into human prisoners. Soon after, they were attacked by a group of Pod infectors, leading to one of the Marines being killed. Lopez, realizing that Smith had been lying, hit him and ordered Mahmoud to search him thoroughly. As he did, they discovered his ONI ID badge, revealing his true identity. However, though Smith outranked the Marines and ordered them to take him off the ship, Lopez would still refuse to leave her Marines behind. Smith then used a concealed knife to kill Mahmoud, stole his rifle and injured Lopez, successfully making his escape. He soon made it to the Marines' Pelican in the cargo bay and escaped the Mona Lisa. Smith was subsequently declared a war criminal by an angry Lopez for his experiments.
As Smith approached the prowler UNSC Red Horse on the Pelican, he attracted the attention of the Covenant assault carrier present in the system. This forced the Red Horse CO, Commander Tobias Foucault, to make the decision to destroy the Mona Lisa with a Shiva-class nuclear missile in order to contain the Flood before the Covenant ship could reach them, dooming any surviving Marines aboard.
After arriving at the Red Horse, Smith was taken into custody on the orders of Commander Foucault for his crimes. Rebecca stated that Smith would be court-martialed for his actions and "maybe even worse," but Foucault knew that if Smith was actually working under ONI Section Three orders instead of on his own as Smith claimed, he'd simply be used as a scapegoat.
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