For other uses of the term "ion", see: Ion.
In their search for the Eye of Jupiter's purpose and symbolism, Lieutenant Gaeta discovers that a nova occurred in the Ionian system which would have been observed 4,000 years ago on ancient Kobol, around the time of the Thirteenth Tribe's exodus. The timing of the nova with the Thirteenth Tribe's journey and its resemblance to the algae planet system's nova suggests to Gaeta that the Tribe's next marker is the Ionian Nebula (TRS: "Rapture").
When the Fleet reaches the nebula, every ship suffers an abrupt power outage. With the Fleet helplessly adrift and without DRADIS, four Cylon baseships also jump to the nebula and launch Raiders. Galactica detects the baseships after power is partially restored, but the Fleet's civilian ships are slower to recover and are unable to make an immediate FTL jump. Galactica responds by launching all its Vipers to intercept the Raiders, and Admiral Adama authorizes the use of nuclear weapons against the baseships. Sortied to defend against the incoming Cylon attack, Lee Adama picks up a mysterious intermittent DRADIS contact and breaks off to intercept it. The bogey leads him on a chase through the nebula's dust clouds and, after outmaneuvering Adama's Viper, pulls up along him portside. Much to his surprise, the unknown contact is the presumed-dead Kara Thrace piloting an unusually pristine Viper Mark II (TRS: "Crossroads, Part II").
During the following battle, the Cylons inflict damage of the civilian ships, destroying the Pyxis and damaging several other vessels, but unexpectedly retreat, apparently after finding out that the Final Five have been activated (TRS: "He That Believeth in Me").
While the Fleet moves closer to the nebula, Saul Tigh, Galen Tyrol, Samuel Anders and Tory Foster experience mutual musical hallucinations. When the Fleet arrives, they are drawn together and come to realize that they are Cylons (four of the final five models). As a group they are able to piece together the song's melody.
Moreover, Laura Roslin, Sharon Agathon and Caprica-Six share a common dream of chasing Hera in each other's presence at the Opera House. Almost immediately after arriving and coinciding with the power loss, Roslin becomes dazed or stunned, possibly because of her use of chamalla extract to induce prescient visions as in the past (TRS: "Crossroads, Part II").
- When an imaginary camera pulls away from the nebula into deep space, it re-enters the galaxy at roughly the same point it exited and zooms to Earth, indicating that Earth and the nebula are not very far apart on a galactic scale.
- Ionia was an ancient region of southwestern coastal Anatolia (in present-day Turkey, the region nearest İzmir,) on the Aegean Sea, which was said to be founded by Ion, son of Apollo.
- In reality, the Ionian Nebula resembles NGC 2440, which is located 4,000 light-years away from Earth.