The Medusa Virus was a synthetic virus created by Kryptonian scientists, Zor-El and Jor-El, to eradicate alien species in case of otherworldly invasions. The virus was never used, as it was a fail-safe mechanism, and the files were brought to Earth on Kal-El's pod.
The Ruling Counsel of Krypton ordered Zor-El to work with his brother, Jor-El, to create the Medusa Virus, much to Jor-El's dismay. Zor-El had no problem creating the virus, however. The virus was a fail safe mechanism to protect Krypton, which eradicates all visiting extra-terrestrial life on the planet.
Stolen by Cadmus
After stealing the files from the fortress, Henshaw goes to the Alien Bar to release a test sample of the virus. It immediately kills all aliens inside. Mon-El was present at the bar as well, but left to follow Henshaw acting all suspicous. They engage in a breif fight.
Believing that Mon-El being residually effected, J'onn puts him in quarantine. Alex puts Kara in quarantine as well, believing the worst about the virus. Mon-El mentions that he regrets not staying at the bar helping the others. Kara tells him that confronting Henshaw was the more intelligent thing to do. The two keep each other company, and Kara watches Mon-El as he gets worse. Kara brings in her adoptive mother to help monitor the situation. While getting close to death, Mon-El and Kara share a kiss.
Later, Kara learned about the origin of the virus at the Fortress of Solitude, doesn't condone her father's actions, as she is now led to believe that both of her parents aren't saints, and it takes J'onn to help her get over her doubts.
Launching the Virus
Cadmus prepares to launch the virus airborne using an isotope from L-Corp. Supergirl tries to warn Lena Luthor about her mother, Lillian, as she is the head scientist of Cadmus. Lena paints Supergirl the truth, as she believes that Lex was the same way before Superman painted him the villain. Unbeknownst to Supergirl, instead of heeding to her warning, Lena concocts a plan to stop Lillian.
She hands over the isotope and swears allegiance to Cadmus, as the two share a mother-daughter moment. The virus-filled missile is launched into the air, but Lena switched the isotope with a subject that neutralized the Medusa virus. Lillian is arrested moments later.
Eliza was later able to reverse engineer the virus and concocts a cure. Mon-El awakens and Kara both play dumb, forgetting about the kiss. But the two of them remember. As well, Eliza was also able to use the cure to eradicate J'onn J'onzz' White Martian blood cells, thus ceasing his conversion.