With Captain Janeway onboard the Borg ship and Commander Chakotay
in command, he is about to bring the captain back, when the captain hails him and orders him to
stop. She announces that she has reached an agreement with the Borg and wants Tuvok's assistance
in working on a way to defeat their new foe, Species 8472.
Meanwhile, Chakotay sees the Doctor about his progress on a treatment on Harry Kim, who is
fighting the Species 8472 disease, which he was inflicted with, earlier. The Doctor tries his
first test and the nanoprobes soon eradicates the disease eating Ensign Kim's body alive. He
soon informs the Commander the Borg may be need more amount of nanoprobes to fight off Species
8472. Uncertain about the Borg alliance, he informs the Doctor to keep the nanoprobe project
inside his matrix and to delete himself in case of any trouble. Chakotay soon learns of Kes's
increasing telepathic ability when she is able to grab a hypospray with a single thought. Tuvok
and Janeway are onboard the Borg vessel working with them to modify a weapon in their struggle
against Species 8472. The Borg appear not to be cooperative, and soon they try to assimilate the
Captain and Tuvok when they can't work individually. Janeway informs them that she will destroy
the information pertaining to the nanoprobe weapon if they assimilate her. The Borg agree to a
compromise and thus assigns drone Seven of Nine to assist the captain and the Vulcan.
While working with Seven Of Nine, it is becoming clear that the Borg are not at all
cooperative. The drone assigned to Janeway and Tuvok are hurrying things along and not even
considering their visitors. Janeway orders Seven to slow down, but does not oblige. It is
apparant that the Borg are hard to work with. Chakotay soon informs Janeway of Kes's condition
and orders him to keep her posted. Soon, Species 8472 is detected off their aft, an attack
ensues. The Borg soon sacrifices their ship in order to protect the nanoprobe weapon they are
developing. During the struggle, Janeway is seriously injured and unconscious, after being hit
by the enery beam.
With Janeway in sickbay, Chakotay takes command of the ship. His first duty is to visit Seven
Of Nine, who along with a handful of drones, have taken shelter in Voyager's cargobay two.
Meeting Seven Of Nine, it is clear that his premonition's about the Borg collective are correct.
They are ill-mannered, uncooperative and selfish beings who want nothing to do except
assimilate. But Chakotay will honor Janeway's request that they need this alliance if they will
ever get out of Borg territory. Soon it is evident that the Borg do not want this alliance and
thus orders Seven Of Nine's drone to rig the deflector dish to emit a quantum singularity, the
homeground for Species 8472. Seven Of Nine escapes cargobay two and into the Jefferies Tube to
begin her work. On the bridge, Harry Kim returns to duty after having been successfully treated
by the Doctor, and informs Chakotay of Seven's actions. Chakotay warns her that if she does not
stop, he will decompress the cargobay, sending the Borg drones out into space. Seven does not
comply, thus Chakotay gives the order to decompress the bay and the drones are sucked out into
space. Seven, however, manages to complete her task and soon Voyager enters the quantum
singularity that is devoid of space, but instead occupied by biological matter.
With Voyager inside the biological mass and Seven confined to cargobay, Chakotay must decide
what to do. Chakotay soon realizes after talking to Seven that the Borg started this war with
Species 8472. The Borg wanted to discover a new realm of space, after finding normal space
boring. Soon Chakotay is informed that the captain has regained full consciousness and wants to
be brought up to date on their current predicament. When Janeway learns that Chakotay has
disobeyed direct orders from his captain, she relieves him of duty and takes charge.
With Captain Janeway back in charge, she uses Kes' telepathic ability to inform Species 8472
of their new destructive nanoprobes. Species 8472 advances on Voyager, and Kes' telepathic link
does not seem to be going too well. Soon Species 8472 attacks Voyager and Janeway orders the
new nanoprobe torpedo launched. They wait as the torpedoes strike the bioship. Nothing seems to
happen for a while, however, split second later, the bioships all explode. It seems that the
nanoprobe weapon have worked. Before there is time to celebrate, Seven Of Nine try to acquire
the nanoprobe weapon and all attempts to stop her fail. Janeway orders "Scorpion" and soon
Chakotay links up with Seven to try and stop her, while the Doctor monitor him and B'Elanna try
to shut down Seven. All hope is giving up when Chakotay breaks through to Seven and B'Elanna
severs Seven's link to the collective. Fazed by the following events, Janeway retreats to the
Leonardo holoprogram to write her log in the old-fashioned way. Chakotay arrives to give Janeway
solace and to determine what can be done about their new passenger - Seven Of
Nine...
