Nyrians capture Voyager and its crew using a translocation system which is capable of transporting two people at a time - one in and one out - and accordingly the Nyrians replace a Voyager crewmember with a Nyrian at regular intervals. Breaking out of the Nyrian prison habitat, Janeway takes control of the translocation system and takes advantage of the Nyrians' susceptibility to a cold environment to force them to surrender.

During the investigation into the mysterious appearance of Nyrians aboard Voyager, Kim and Torres discover no clue from internal sensors in the corridor where the Nyrian appeared (Deck 6). Kim initiates a level 1 anaylysis on exterior and interior sensor readings at the exact moment of the first Nyrian's appearance (1132 hours).

While the lengthy Nyrian invasion takes place, the nearest inhabited world to Voyager is over ten light-years away.

Tuvok increases shield strength but reports that it has no apparent effect. He says, "However-" but at the moment he vanishes (translocated by the Nyrians).

Janeway orders security details at every access point. Later all but essential functions are to be shut down.

Torres detects a field of polaron particles around Kim at the moment he vanished but the field disappeared when he vanished. Later she initiates a tetryon scan shortly before she is translocated off Voyager by the Nyrians sooner than she would otherwise have been, because she is getting too close to the truth.

When the Nyrians outnumber the crew almost two to one, Chakotay orders access to all systems restricted to authorised voice-prints only. He also orders sealed off any part of the ship not in use (including Decks 11 to 15) and orders security forcefields around sensitive areas such as the warp core, the armoury (Deck 6: [#74 The Raven]) and the torpedo bays. Status and access to ship's systems can be done at a corridor wall monitor.

Chakotay discovers from a corridor wall monitor that the Nyrians are taking key systems

When Ensign Lang is left in command on the bridge, she orders the few remaining crew there to start by reinforcing the containment fields and re-route emergency power as they have to seal the bridge doors. They do not have time to do this and the Nyrian boarding party captures the bridge.

The hatch from the Jefferies tube network into the cargo bay is seen in this episode. The hatch from the Jefferies tubes into sickbay is also seen in use (seen also in [#157 Shattered]).

Chakotay enters sickbay from the Jefferies tubes

open hatch; view into part of the Jefferies tubes from the cargo bay

Unknown to the Voyager crew at the time, deterioration of or actual damage to ship's systems occur as the result of activity by Nyrians and by Chakotay and (possibly partly) by Crewman Gennaro prior to the Nyrians' total capture of ship and crew. These are: Ensign Lang (acting chief of security) reports what "looks like a circuit relay malfunction" on Deck 4 which causes a problem with the internal sensors.

Ensign Lang reports: "Decks 11 through 15 are completely shut down. Most of the remaining crew are on security details near the cargo bay and shuttlebays." At this point Voyager is operating on a skeleton crew of just 14, being the 12 that Lang reports, Lang herself and Chakotay, although it is not known if she includes or excludes the Doctor.

During Chakotay's sabotage of the ship, as he starts to access systems from within the cargo bay the computer warns that disabling lateral EPS relays may disrupt computer functions throughout the ship.