The Ocarina was eventually destroyed by Nagate Tanikaze.
Like all Mass Union Ships, the Ocarina contains a merged True Body surrounded by a large amount of Placenta. The Ocarina contains approximately 5,000 True Bodies, though it can split some True Bodies off into individual Gauna for attack purposes. Some True Bodies remain on the surface as well, with over 400 True Bodies destroyed by Guardians during their initial assault.
The Ocarina contains the biology for an immense Heigus Particle Cannon, sufficient to destroy the Sidonia. Calling upon the stored Heigus particles within its remaining 4,500 True Bodies, it was capable of firing an immense beam of Heigus Particles at Sidonia.
Internally, the Ocarina's merged True Body resembles first an amebic ball, which then changes to an approximate human face. Whether this face would be able to talk to humans or not, and whether the Ocarina contained an intelligence capable of speech, is unknown.
The Ocarina pestered Sidonia for some time, launching attacks against the ship and sending out Gauna to assault Guardian squads. Its role seemed to center around shadowing and observing Sidonia, as it refrained from direct assaults until the debut of Tsumugi Shiraui. Once Tsumugi debuted, it entered the battle in earnest.
Determining Tsumugi to be the greatest threat, the Ocarina sent out 60+ Gauna, which enveloped Tsumugi and forced her to fight desperately to survive. After those Gauna were defeated, it reached out to destroy Tsumugi, only to find itself facing many Guardian units with threefold ammunition for their GCPDS systems. After losing roughly 10% of its True Bodies, the Ocarina morphed and developed a massive Heigus Particle Cannon. It was only due to Tsumugi's heroic deflection of the beam that Sidonia was not destroyed.
Nagate flew into the interior of the Ocarina, convinced that the only way to stop Sidonia's destruction was to destroy the Ocarina's merged True Body. Meeting the True Body, he was able to pierce it with multiple GCPDS shots, foaming the Ocarina and ending the threat to Sidonia.
In the anime, there are no Ocarina. But, it's role replaces by the colonist ship shaped-like gauna. Nagate put distance between himself and the gauna before flying towards it at high speed and jettisoning his engine. The engine flew into the Heigus Particle Cannon, causing a massive explosion which exposed the Mother Core within. This allowed the remaining Guardians to fire on it directly, destroying it.