In late 2259, the G'Tok was scouting for potential targets in enemy space when the Centauri attacked the Narn Homeworld. After the Centauri forced the Narn government to surrender, the G'Tok and her crew became fugitives. They were hunted by Centauri forces for months before they finally arrived at Babylon 5. The ship's captain Na'Kal asked Captain John Sheridan for sanctuary and assistance with repairs. Sheridan agreed to this request.
Unfortunately, at exactly the same time, representatives from the Earth Alliance were negotiating a non-aggression pact with the Centauri. Word of the cruiser leaked out to Frederick Lantze of the Ministry of Peace, who in turn informed Centauri ambassador Londo Mollari. Londo contacted his people, who responded by sending a Primus class battlecruiser to capture the G'Tok.
When Sheridan refused to hand over the G'Tok, the Centauri cruiser opened fire on Babylon 5. The station and its Starfury squadrons returned fire and destroyed the cruiser, allowing the G'Tok to escape. When Lantze berated Captain John Sheridan over this incident, Sheridan cited General Order 47 which required Earthforce personnel to assist distress calls from any ship not engaged in hostilities against Earth. Mr. Welles, of Nightwatch, confirmed that he was correct in his interpretation of the regulations, but insisted the captain make a public apology in order to smooth out diplomatic relations. This "apology" (which would have been very sarcastic) was never delivered due to an assassination attempt on Sheridan by a pair of unknown Centauri.
Remnants of the Narn Fleet not destroyed or interned by the Centauri eventually joined the struggle against the Shadows led by John Sheridan, the heavy cruiser G'Tok in particular playing a pivotal role in an early engagement in 2260.
Needing ships to aid in the defense of the station, John Sheridan and G'Kar invited the G'Tok to come to the station. G'Kar meets with Na'Kal and discuss postponing an open strike against the Centauri. When Sheridan seeks to test their theory regarding the Shadow's vulnerability to telepathy, G'Kar asks Na'Kal to have the G'Tok provide escort to the White Star. Na'Kal refuses, feeling it is surely a suicide mission and not wishing to risk one of the few Narn vessels still functioning. After Sheridan embarks on the mission, Garibaldi comes to G'Kar while he sleeps, angrily confronting him about not forcing Na'Kal to go forward. He returned the Book of G'Quan and tells him that the responsibility lies with G'Kar. Accepting what Garibaldi has said, G'Kar convinces not only Na'Kal but a host of other League members to mount a small fleet and rescue Sheridan.
What ultimately happened to the G'Tok after the Shadow War and the liberation of the Narn Homeworld is unknown. It can be assumed, however, that she continued to serve her people as they rebuilt.