The Nightingale was the name given by Ensign Harry Kim to the Kraylor starship Medical Transport 136, previously under the command of Captain Brell. The Nightingale differed from other Kraylor medical transports in that it was used on a secret mission by a research team to transport a cloaking device developed for their fleet.
The crew of the USS Voyager first came across this vessel in early 2377 when the Delta Flyer II responded to a distress call from the commander of the Kraylor vessel. Responding to the signal, Kim discovered the Kraylor were at war with the Annari Empire, and were under attack by Annari warships. Kim tried to negotiate with the Annari, but was forced to disable their vessels when he found himself under attack.
After beaming onto the Medical Transport 136, Kim and Neelix found the vessel in complete disarray – about half the crew were dead, including all but one of the bridge officers. Kim offered to help with repairs of the vessel, along with Neelix and Seven of Nine.
After the vessel had been repaired, Loken, head of the research team, begged Kim to captain the vessel back to their homeworld, telling him that the vaccine they have been working to develop must reach there. Kim was reluctant, not wanting to violate the Prime Directive, but finding out that the planet where Voyager had landed was en route, agreed to take them that far at least.
Captain Janeway was eventually convinced to take the Kraylor's side in the matter, and permitted Kim to take command of the medical transport, which he promptly renamed the Nightingale. As Kim himself admitted, he named this vessel for Florence Nightingale, whom he described as being known for aiding wounded soldiers on the battlefield – an appropriate name for this vessel, which he believed was delivering vaccines to their homeworld. However, Janeway asked Seven of Nine to go along on the journey. Kim was excited at the chance of having his "first real command."
The cloak began to fail a short time into the journey due to a fluctuation in the propulsion power systems. Repairs were made, yet Kim dismissed Seven's recommendations to run a full diagnostic, reminding her Janeway wanted them back before Voyager finished repairs. A short time later, as predicted, the primary generator failed, as did the cloak. Half a dozen Annari vessels moved into attack range, and a Kraylor researcher named Dayla volunteered to try and bring the cloak back online, receiving instructions from Kim, and she and Loken together figured out how to bring the cloak back online by taking the warp core off-line. Unfortunately for Dayla, life support failed in the engineering area, and she died.
Confronting Loken, Kim discovered the Nightingale's cloak was actually a prototype, what Loken's team, including Dayla, had really been working on at a secret base. The Annari knew about the prototype, and didn't want it to arrive at the Kraylor homeworld. Kim realized that he was in the middle of a breach of the Prime Directive, and ordered the Nightingale to reverse course, but was relieved of command. Seven of Nine pointed out to Kim that if he truly cared about the crew, he needed to help the Kraylor home, or they may not survive.
At the Kraylor homeworld, a new series of scanning pulses illuminated cloaked vessels. Having been detected, surrounded and outgunned by Annari vessels, Kim took command, promising to help them, to which Loken agreed. Realizing the situation, Kim appeared to offer a conditional surrender with the Annari; however, if they didn't allow the scientists to safely evacuate to the planet, Kim threatened to destroy the Nightingale. Loken was furious about Kim's apparent betrayal, but was assured he had a plan to save the vessel, but if he failed, "...at least the scientist who designed the cloak will be alive to create another one." Once under the grip of the Annari tractor beam, Kim reversed the Nightingale's shield polarity, and used the momentum to outrun their pursuers to the defense perimeter.