As he set the TARDIS into orbit over Caprica, he stared grimly down at the planet that was about to be destroyed.
Of all the sins he'd experienced in his long travels throughout time and space, what he was witnessing here was unquestionably one of the greatest. He could sympathise with the Cylons' anger at how they had been treated by the Colonials at first, but it wasn't as though their scientists had set out to create a sentient race for the sole purpose of enslaving it, and the Cylons couldn't hold twelve whole planets responsible for the actions of their creators…
Unfortunately, as much as he hated what had happened, there was nothing that he could do to stop the destruction of the Twelve Colonies. Not only was it part of established galactic history, but it was a part of his own personal history; even if he could tweak one, changing his own past was completely impossible.
However, just because he couldn't change anything didn't mean that he couldn't help to make sure that things worked out the way they should in the aftermath; it was the reason he'd come all this way with the data storage device he was carrying in his pocket.
Computers might be a variable strength of his across his various incarnations- his first incarnation had been particularly good at it while his sixth had needed help to work with the computers of the 1980s- but even if the Daleks' computer defences were too advanced for him to hack them that easily, it wasn't as difficult for him to penetrate the Cylons' defences, made even easier by the fact that they weren't expecting anyone to fight back in this manner and he had no real need to worry about whether or not he left any traces for someone to discover later. Combined with the fact that he was using a copy of a particularly advanced artificial intelligence- it wasn't as advanced as the first Voractyll he'd created, but it shared enough of that one's programming to make the same impact- it shouldn't be hard to immobilise a race of machines that had never expected they'd have to deal with something capable of breaking their firewalls in the first place.
As he materialised the TARDIS in a quieter part of one of the main Cylon baseships, he walked out of the police box and plugged the storage device he'd used for Voractyll into the ship's primary computer system. Given the interconnected nature of the Cylon systems, once it had infected this ship it wouldn't take long for it to pass to the rest of the fleet, and then both Cylon and Colonial ships would basically be left in the same position, their guidance systems virtually useless and able to do nothing more than fire when they were pointing in the right directly.
With both fleets essentially paralysed, the Cylons would still manage to take out the Colonial ships given that they had the advantage of forward planning, but their superior numbers would just give the Colonials more targets; even relatively random shots would be able to do enough damage to wear down the fleet eventually.
Unleashing the virus now wouldn't be in time to save the majority of the Colonial battlestars, but by acting now, he would leave the Colonials with just enough of a chance to strike back at their renegade creations, wearing down the number of baseships that would manage to survive this encounter in return. Even if most of the Cylons were able to download into their resurrection ships, they still wouldn't have enough baseships to provide the surviving Cylons with adequate space to be a threat. The new bodies could be grown fairly quickly, but the baseships required far more time to construct, and the Cylons wouldn't feel a particular need to rebuild with only two battlestars and assorted civilian ships left to worry about.
He couldn't save the Twelve Colonies of Kobol, but by doing this now, he would make things easier for the surviving Colonial Fleet by giving them fewer baseships to fight their way through until the Cylon Civil War… as well as giving their future ally less enemies to try and reason with…
It wasn't going to be the easiest time he'd ever had, but amid all the chaos of his attempt to avoid the Time Lords and keep Compassion safe, his time with the Colonial Fleet would be the most rewarding experience he'd have during that time; if he could ensure that he had an easier time of it, what was wrong with that?
AN 2: For the record, part of this story was inspired by another 'Galactica' fanfic series I read (I won't name names because I disagreed with more points than I liked, but this point got me thinking), which noted how implausible it was that the Cylons were able to destroy the Twelve Colonies and yet had such a small fleet to deploy against the survivors after that assault. While I didn't agree with the writer's interpretation of the idea that certain Colonial officials had known about the imminent Cylon attack and just let it happen while ensuring that there would still be survivors- Cavil was an arrogant ass, but he wouldn't have sent in the human-form Cylons until he was certain they would be undetectable- they did make a valid point that the Cylon fleet we saw in the show was very small, so it just made sense to come up with an explanation for what happened to the rest of their fleet
AN 3: For those wondering, the reference to Voractyll is a reference to the Fourth Doctor novels 'System Shock' and 'Millennium Shock' where the Doctor stops a race of alien cyborgs known as the Voracians from turning Earth's technology against humanity; Voractyll was the computer program they would use to 'liberate' the machines, but the Doctor stopped their first attack by acquiring a copy of Voractyll and convincing it of the superiority of the organic, with the result that it not only destroyed the Voracians' Voractyll, but was then used to reconfigure the Voracian ship so that it was rendered unable to do anything but crash
AN 4: Watch this space; the first chapter of the Eighth Doctor's adventure with the Fleet will be up soon.