Note: I might have put way too much information here; I've bolded the most important things.
Okay so here's the situation (this is the context in story; I'll bold the actual question): the Solar Federation has sent Solfleet 7, which has twenty-five ships, to take out the Titanean Order. The events of this scene take place in orbit around Saturn, near the orbit of Iapetus.
After the fleet spreads around the system, the three Sirius-class ships (the biggest, baddest things in the solar system; their main weapon is a massive 2GW Particle Beam mounted inside the ship, which is somewhat cylinder-shaped), two fuel ships, and one medical ship, which are still grouped together, are approached by a puny ship, the Saboteur from the Order.
The captain of the Saboteur antagonizes the Admiral of Solfleet 7 into ordering one of the Sirius ships, the Leopard, to fire on the Saboteur. The Leopard, though, has an explosion on the bridge that seems to have been caused by the particle beam.
Here's my current explanation of how this happened: The Leopard was hacked by the Saboteur and its targeting instructions were changed.
My current process for how that happened involves nanomachines latching onto the medical ship (which is older with less robust security) and exploiting the way that Federation ships can be remotely detonated (by the Admiral to combat mutiny in extreme situations) to alter the beam's code. I need a better way for the Saboteur to hack the Leopard. Your resources:
The Titanean Order has hired the engineer who was in charge of designing the Sirius-class battleships. This means they will have access to detailed technical details of how the Leopard's systems worked.
They've been spending tons on developing this technology, so spare no cost.
You have a maximum of three people to monitor and guide the hacking process. The Saboteur has a five-person crew, and two of them are the Captain (who will be talking to the Admiral over radio) and the Pilot (who will be flying the ship). I'd love to have an extra person available if that's possible; so bonus points if you can do it with two people.
The Saboteur will be thirty meters long (probably 15 wide/tall? That's a bit variable. It should look like a normal shuttle.) and use chemical propulsion. Assume that you get, say 2,500 m^3 to put equipment and crew working space in. If you need a giant heavy thing (other than, say, a huge computer for cracking cryptography) it probably won't work. The lighter, the better.
You may, if necessary, change the storyline within reasonable limits to accommodate your idea.
The best answer will:
Provide a full explanation of how the hack is carried out. You may use my own concept, altered to make it more believable. This all takes place about 150 years from now, so use appropriate technology (bonus points if they use some retro technology no one in that time period remembered).
Provide a plan that will thoroughly spook the bewildered Admiral (this is made easier by the fact that her best friend is killed in the explosion; you can factor in some emotional trauma) enough to surrender the fleet. (i.e. This should be something she believes they can do again, to other ships.) To help, note that the Leopard's particle beam was successfully tested before departure and locked down until about an hour before arrival, eliminating the possibility of sabotage (which would likely not be repeatable).
Explain the resources needed to complete the plan.
Good luck! Ask me if you have questions or need clarification.