There is a hull breach on deck 11 section 3. Kim says the damage is minor: it appears a plasma conduit overloaded. Then a bulkhead collapses in Jefferies tube 84; Kim says it was caused by no power surge or systems failure, as the plasma network is stable. Investigation shows that an intruder has entered the ship. A blood sample found at the scene indicates it is a member of Species 8472. The crew goes on alert, but an engineering team is attacked before they can fully lock down the area. The Hirogen hunting the member of Species 8472 informs Janeway that if he is not allowed to continue hunting the alien, he will allow the approaching Hirogen ships to destroy Voyager. The Hirogen is allowed out of sickbay to located the intruder. They learn the intruder boarded Voyager as part of an attempt to open a singularity into fluidic space, its home. Through telepathic contact with Tuvok it explains it was trapped, alone and injured, after its ship was damaged during a conflict with the Borg. Janeway asks Seven to open a singularity but Seven, believing the alien to be dangerous, refuses to help. Approaching Hirogen ships fire on Voyager and as a result forcefields go offline, enabling the Hirogen (confined to sickbay) to escape. The Hirogen finds its prey and, as they struggle, Seven (disobeying orders) taps into transporter controls and beams them both to one of the Hirogen ships where the kill will surely occur. The Hirogen immediately stop firing and leave.

Torres erects a level 10 forcefield around engineering and sets up secondary forcefields around every hatch, Jefferies tube, and conduit leading into the room. She orders all the consoles secured to accept authorised command codes only. She begins to lock down the warp core by having an ensign re-align the dilithium matrix to a frequency of 3.96, but is interrupted by the attack by a member of Species 8472. Species 8742 accesses engineering through the antimatter injector port and escapes through Jefferies tube 17-Alpha.

right of picture: the starboard docking port on the primary hull

close-up of the docking port

ceiling and ceiling lights above the warp core in main engineering;
this is the moment when the member of Species 8472 dives downwards

Tuvok holds the alien down on Deck 11 Section 94. Deflector control is on Deck 11, Section 59. Species 8472 accesses environmental controls and shuts off life support, including artificial gravity, on Deck 11. The security detail sets up headquarters on Deck 10, Section 12.

Paris claims that he once tracked a mouse through Jefferies tube 32.

Ship's weapons have little effect on Hirogen hull plating. This follows on from [#83 Hunters] in which it is established that Hirogen hulls have monotanium plating which scatters Voyager's transporter targeting beam. The crew diverts warp power to the phaser banks to try to penetrate Hirogen hull armor.

Seven accesses transporter controls

Seven refuses Janeway's order to open a singularity and allow the alien to escape to its realm. Instead Seven accesses transporter controls from a hallway on Deck 11. After Seven beams the alien to the Hirogen ship, Janeway restricts her access to any primary systems on Voyager without her direct authorisation. Janeway admits to needing her help in the astrometrics lab, if she is willing, otherwise she is to stay in the cargo bay.

Because ordinary phaser fire is ineffective against Species 8472, Seven modifies phaser rifles with Borg nanoprobes to incapacitate the alien.

Species 8472 emits a bio-clectric field, making it impossible for the Doctor to scan with a medical tricorder.

EVA (extra-vehicular activity) suits, known as environmental suits, are seen again in this episode, first seen in [#71 Day Of Honor].

A hull rupture on Deck 11, Section 3, is read by sensors as a plasma conduit overload, but it turns out to be really where Species 8472 entered the ship. The bulkhead collapses in Jefferies tube 84. A direct hit to the EPS manifold knocks out main power and takes forcefields on all decks offline until auxiliary power goes up a moment later.

Voyager is crippled by direct hits from Hirogen ships to both warp nacelles.

Access to primary and/or secondary starship systems can be distinguished in order to allow personnel access to one or the other or both.