Story
Knowing the war with the Borg was nearly won, Picard was on a mission far from home to eliminate any known remaining Borg when the Enterprise E happened upon a strange and unresponsive Borg cube. An away team was sent, and returned with the unusual news that all systems except life support on the enemy ship were down, nothing was moving, and the structure of the ship altogether had differences that did not register as Borg technology, or anything even recorded in the Starfleet database.
The team also brought back the Borg primary computer core module and a strange metal relic with alien runes etched across it, which was assumed to be part of the new tech the Borg must have assimilated that caused their shut down.
Before leaving the area, the disabled ship was destroyed, but it took a surprising number of quantum torpedoes and phaser streams to finally do so, as it seemed to self repair at an alarming rate.
Within a few days, the Enterprise crew had deciphered enough of the Borg computer data to have the coordinates of the relic's origin, and a course was set at warp 9 to reach a never before explored sector of space. With any luck, they would locate a new planet with life and discover what the Borg were up to.
The journey was long even at top speeds, and over the days the crew began to report odd structural changes in various locations all over the ship with no one claiming responsibility for any of them. Geordi confirmed that entire ship was indeed changing, but it all seemed to be upgrades and everything new was made from an incredibly strong new metal, quite similar to the alloy the relic was made from.
Picard feared the alien device might be attempting to take over the ship, and ordered it jettisoned immediately, but none of the doors to airlocks or transporter rooms and controls would open. As the crew tried to stay calm and analyse the situation, the ship eventually shut down completely, except for life support and artificial gravity...
For nearly 36 hours the ship sat in darkness, its crew terrified and helpless to do anything at all as the ship slowly grew new parts and systems before their eyes. The enterprise got longer, its shield matrix became at least twice as powerful, 4 new powerful impulse engines twisted into shape under the rear of the saucer section that would surely improve maneuverability greatly , and the computer seemed to be reading through all of its own information over and over... Until nearly everything simply came back online.
Picard was back in control, and everything seemed back to normal aside from the obvious improvements, communications were still down, and the computer seemed to now be possessed. Both Picard and Riker had many questions, but the computer would only say "I will protect you. You must reach Cybertron.", over and over.
With little other choice, they resumed their course.
Arriving sooner than expected, the Enterprise came upon a metal planet which was surrounded by over a dozen Borg cubes! Knowing there was little chance to defeat them alone, the Captain tried to change course and go to warp, but a powerful, rumbling voice over the ship intercom said, "Trust me, friends" and suddenly everyone in the saucer section was teleported to the main body of the ship, the captain and high ranking crew members in their respective positions on a new and improved battle bridge.
Everyone braced themselves as the ship shook and jolted, its parts moving around to a drastically new configuration as the Borg ships closed in and opened fire.
Soon, the Enterprise had become a enormous humanoid robot, easily dispatching the Borg ships one after another, some cleaved with the plasma blade on its right arm, some crushed into one another by the huge shield mounted on its left arm, and many destroyed by the phaser banks in its eyes, and the quantum and photon torpedoes that fired from its right shoulder and chest.
The bridge crew witnessed on screen the amazing show of power until not one Borg ship remained.
There was no doubt now, the ship was alive, and was a more than welcome ally to the Federation.
"Who... are you?" Picard asked.
The voice over the intercom answered him. "I am NCC-1701-E. I am the Starfleet Soverign class ship, Enterprise. I am... an Autobot."
"Autobot E, then" Riker said with a sly smile.
