I had the idea for a series about a Federation ship, maybe an Enterprise, that's designed to be the first to go across the galactic border, and into another galaxy.
But as they travel across, they encounter an invasion fleet.
The first attack of the enemy wipes 99% of their computers. There's only a skeleton crew (why have a huge ship full of people, when you only focus on an handful) on the ship, and when they get back, noone seems to believe them, (are there infiltrators ahead of them? Was there really an invasion force or were they halucinating? (as is assumed by the Federation, there's energy from the attack in the crew's brains as well as the ship, it's scrambled many systems, and is assumed to be from the barrier, not the attack)
Seeing as the ship is incredibly fast, it's the only advantage the crew has, they steal the ship and set out to prove themselves right.
The Aliens arrive, and prove to be very deadly, a full salvo from their "main weapon" wipes all computers, leaving a ship dead in the water, with nothing. Not even life support. The ships are then taken by the invaders and crewed by the aliens.
Nothing can stop the "main weapon" not shields, not a cloaking device, nothing. Even the Jem Hadar are suffering from the Invaders attack.
There seems to be no rhyme or reason to the invasion, they go from one system to another and another randomly. DS9 holds out, but only because it's large enough and open enough to hold enough oxygen for a skeleton staff to reboot the systems.