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Tracking a shuttle's distress signal to the nearly deserted Arbuk System, the USS Voyager crew encounters an unusual weapon a thousand times more powerful than the starship. Inside, the crew discovers an unconscious alien and no more information about the device. Soon Captain Janeway and her crew are attacked by a group of mysterious warships with an interest in the weapon's power. Now, with warp power offline, the crew of the Starship Voyager must find a way to save themselves from a group of aliens desperate to control the weapon…

For ages they have sought to claim our worlds. Now, at last, we take the battle to them… Far from the Federation's desperate war against the Furies, the crew of the USS Voyager encounters something they never expected to hear again: a Starfleet distress call. The signal leads them to a vast assemblage of non-humanoid races engaged in a monumental project of incredible magnitude. Here is the source of the terrible invasion threatening the entire Alpha Quadrant — and for the Starship Voyager, a possible route home. But soon there may be no home to return to… The epic conclusion to the greatest crossover saga of all time!

To protect the cargo ships essential to the continuing existence of the fledgling Coalition of Planets, the captains of the United Earth's Starfleet are ordered to interstellar picket duty, with little more to do than ask "Who goes there?" into the darkness of space. Captain Jonathan Archer of the Enterprise seethes with frustration, wondering if anyone else can see what he sees. A secret, closed, militaristic society, convinced that their survival hangs by a thread, who view their neighbors as a threat to their very existence – the Spartans of ancient Greece, the Russians of the old Soviet Union, the Koreans under Kim Il-sung – with only one goal: attain ultimate power, no matter the cost. The little-known, never-seen Romulans seem to live by these same principles. The captain realizes that the bond between the signers of the Coalition charter is fragile and likely to snap if pushed. But he knows that the Romulans are hostile, and he believes they are the force behind the cargo ship attacks. If asked, Archer can offer no proof without endangering his friend's life. To whom does he owe his loyalty: his friend, his world, the Coalition? And by choosing one, does he not risk losing all of them? What is the solution to a no-win scenario?

Without warning or provocation, a Xindi weapon appears above Earth and unleashes a blast that kills millions across two continents. It is only the first such weapon: a second is being built, and this time it might very well destroy the entire planet. Desperately trying to save the Earth and her people, Starfleet must, in a heartbeat, change its mission from one of peaceful scientific exploration to one of military service. There is only one ship fast enough to stop construction of this new weapon: the Starship Enterprise. But its crew can't do it alone. Captain Jonathan Archer accepts aboard his ship a contingent of Military Assault Command Operations personnel: battle-hardened soldiers known as MACOs. Starfleet and the MACOs are two different services now sharing a common goal, but they are divided as to how to reach it. It is a culture clash that echoes across the centuries of military service. The men and women now aboard Enterprise know they must succeed in working together or the price will be paid in the blood of innocents. Failure is not an option.

When an alien pirate abducts Kes, USS Voyager takes off in hot pursuit, but the first rescue mission fails disastrously; an ion storm forces the shuttle to crash on an unknown world. Now Captain Janeway and her away team must embark on a hazardous trek through a hostile environment in search of a way off the planet, while Voyager, commanded by Chakotay, confronts an enemy fleet in the depths of space.

The USS Enterprise-D journeys to Lorca, a beautiful world with a feudal culture where the inhabitants wear masks to show their rank and station. There, Captain Picard and an away team don masks of their own to begin a quest for the planet's ruler and the great Wisdom Mask that the leader traditionally wears. Their mission: to establish diplomatic relations. But shortly after transporting, Picard and his party lose contact with the ship, and Commander Riker leads a search party down to the planet to find them. Both men, however, are unaware that their searches – indeed, the ship's entire mission – are part of a madman's plan. A madman who is setting the stage for a trap that will ensnare both the Enterprise landing parties, and leave him poised to seize control of the awesome Wisdom Mask…