The Enterprise responds to a distress call from a Federation colony, but arrives to discover the colony gone, with only a crater remaining. Based on past knowledge of what happened to colonies along the Romulan Neutral Zone and on a deserted planet in System J-25, the Federation suspect Borg activity.
Admiral Hanson arrives with Lt. Commander Shelby, an expert on the Borg, who assists the crew in determining the cause of the colony's disappearance. Hanson informs Captain Picard that Commander Riker has been offered the command of a starship, the Melbourne, for the third time, and suggests that Riker take the position. Although there is tension between Riker and Shelby, who intends to take over his position of first officer of the Enterprise, they confirm the colony was assimilated by the Borg. Hanson advises Picard that another Federation vessel encountered a strange "cube-like" vessel before sending a distress call that ended abruptly. The Enterprise moves to intercept and confronts a Borg Cube.
The Borg demand that Picard surrender himself, which he refuses. Although initially deterred by the Enterprise's shield modulation, the Borg lock the vessel in a tractor beam and begin cutting open the hull. Shelby suggests randomly changing the frequency of the ship's phasers to prevent the Borg from adapting to the attack, which frees the vessel. The Enterprise escapes to a nearby nebula, with Chief Engineer Geordi LaForge and Ensign Wesley Crusher adapting a technique suggested by Shelby to modify the deflector dish to fire a massive energy discharge capable of destroying the Borg cube. The Borg flushes the Enterprise from the nebula with magnetometric-guided charges, and then board the ship and abduct Picard. The Borg Cube moves off at high warp speed towards Earth, with the Enterprise in pursuit.
Riker, now in command of the ship, prepares to join an away team to transport to the cube to rescue Picard, but Counselor Troi reminds him his place is now on the bridge. Shelby leads the away team onto the Borg cube, where they discover they are ignored. The team locate Picard's uniform and communicator, and then destroy power nodes inside the cube, forcing it out of warp. As the team prepares to transport to the Enterprise, they see an assimilated Picard. The Borg contact the Enterprise, with Picard stating he is now "Locutus of Borg", and to prepare for assimilation. Riker orders Worf to fire the deflector dish.
The deflector dish has no effect, with Locutus revealing that, as he is in possession of Picard's knowledge, the Borg had prepared for the attack. The Borg cube continues at warp speed towards Earth, with the crippled Enterprise unable to follow. Upon reporting their failure to Hanson, Riker is promoted to Captain and advised a large fleet of starships is massing at Wolf 359 to stop the Borg. Learning via subspace communications that the battle is going badly, the Enterprise eventually arrives at Wolf 359 to find the fleet has been destroyed (including the Melbourne).
The Enterprise follows the cube's warp trail, and offers to enter into negotiations with Locutus. The request is denied, but the communication reveals Locutus' exact location within the cube. The Enterprise locates the Borg cube, and, as per a plan suggested by Shelby to Riker, separates into saucer and stardrive sections. Although Shelby suggested attacking with the stardrive section, Riker does the reverse and orders the saucer section to fire an anti-matter spread near the cube, disrupting its sensors and allowing a shuttlecraft piloted by Commander Data and Lt. Worf to pass the Borg shields and beam aboard the Borg cube. They successfully kidnap Locutus, although the Borg ignore this and continue to Earth, destroying all resistance.
Data and Dr. Crusher create a neural link with Locutus to gain access to the Borg's collective consciousness. Data attempts to use the link to disable the Borg's weapons and defensive systems, but cannot, as he discovers they are protected by password. With the Borg on the verge of invading Earth, Riker orders the Enterprise to ram the Borg cube, but Data asks him to wait. Picard breaks free from Borg control and tells Data to "sleep". Data issues a low-level, unprotected command to the Borg to enter sleep mode, causing their weapons and shields to deactivate. A feedback loop builds in the Borg cube which destroys the vessel. Dr. Crusher and Data are then able to successfully remove all Borg implants from Picard.
The Enterprise moves to an orbital shipyard for extensive repairs, and Riker, although offered command of his own ship, insists on remaining as the first officer. Shelby is reassigned to a task force dedicated to rebuilding the fleet. Picard recovers slowly but is still disturbed by his ordeal.
The first episode won Emmy Awards for "Outstanding Art Direction for a Series" and "Outstanding Sound Editing for a Series".
The storyline appeared in TV Guide's "100 Most Memorable Moments in TV History" (July 1, 1996), ranked number 50. The episode was also ranked #70 on the 100 Greatest TV Episodes of All Time.
In 2008, Empire magazine rated Star Trek: The Next Generation 37th on their list of "The 50 Greatest TV Shows of All Time" and cited "The Best of Both Worlds, Part II" as the show's best episode. The episode was ranked #36 on TV Guide's list of "TV's Top 100 Episodes of All Time". The two-episode arc ranked second in Entertainment Weekly's list of top 10 Star Trek: The Next Generation episodes.
These two episodes, prepped for Blu-ray release and to promote the release of the Season 3 on Blu-ray, were combined with interviews and outtakes and shown as a one-night only event in movie theaters across USA and Canada on the night of April 25, 2013.