When Voyager comes across a large debris field, the crew's research leads them to conclude that it is all that remains of the Vostigye scientific space station they were heading for. Finding a strange trail of plasma particles at the site, they set course to solve the mystery of what could have destroyed the station. As Voyager follows the particle wake, an astral eddy that has formed at the confluence of space and subspace rips out of subspace and bears down on the ship. They come through the anomaly fairly unscathed. Chakotay suggests that the next time an astral eddy appears, they capture some if its highly charged plasma particles. Paris suggests that taking a shuttlecraft into the wake of an eddy might offer the best opportunity to capture the valuable plasma particles. When another one forms, Paris attempts the maneuver, in the shuttlecraft Cochrane, only to be caught up in another astral eddy and, to the watching Voyager crew, disappears within the eye of the astral phenomenon. Trapped between space and subspace, in the spawning area of the eddies, Paris decides that the only way out is the way he came in, inside a space tornado. As a huge storm crosses into space, Voyager manages to beam Paris aboard.

The energy from the plasma in the astral eddies could supply extra power, allowing the crew to go off replicator rations for a while. After sending a probe into the anomaly they learn that it has a temperature gradient of 9 million kelvins, massive discharges of plasmatic energy, and a perfectly calm "eye" in the centre. Apparently some of the matter inside it is being exchanged between space and subspace. The eddies originate from an unstable interfold layer between space and subspace. It is possible to modify the Bussard collectors to gather plasma particles, but Voyager's energy emissions are so high they would corrupt the particles.

The shuttlecraft Cochrane's hull begins to buckle and breach, but it is ultimately beamed safely to the shuttlebay.

Propulsion and navigational control are offline and transporters also go offline for a time. There is a minor buckling of the hull on Deck 3.