Alright so i have a plan for an adventure that is horrorish the story short is the pcs come across an old ship sending out a distress signal the pcs board and are attacked cutting them off from their ship. The ship is filled with rakghouls yet the lower levels not contaminated it turns out a mad scientist is attempting to control rakghouls to create an unstoppable army. The pcs find his controll room and put a stop to his plans. They then enact a safeguard that gasses the whole ship killing the rakgouls. How could this be improved

Perhaps the party triggers the failsafe manually prior to accessing the lower, 'safe' decks. Then they find out it was only a specialized knockout gas (getting test subjects isn't cheap) and realize that the problem is about to get a LOT bigger. Vicious fight to the vessel's reactor, some 'creative maintenance' to make said reactor very cranky, then some sort of timed escape.

YMMV though.

First off how have they recreated the Rakghouls or did they acquire a couple say by securing some infected mercenaries and during the trip their numbers expanded because they didn't properly secure the holding facilities since the rakghoul virus is being spread through the air ducts and not properly neutralised?

The main villain thinks he's controlling them when in truth a few of them developed intelligence and is using the villain's lunacy to make it look like he does until they can catch the new arrivals off guard and seize their ship so they can escape to infect anywhere they can...

This works better if your PCs have rivals chasing the same thing so your PCs can escape aboard their own ship to pursue the Rakghoul infected ship even as the Imperials attack the villain's ship.

To make it more climatic have 3 imperial frigates chasing the villain's ship before turning their guns on whatever they assume is infected including the world below... now your PCs have to find a cure, get back to their ship and escape the impending bdz with the threat the Empire will put a Death mark on their ship believing they're infected too!

Now the question is how to cure them if infected?

Maybe they're already ill and unaware its rendered them immune to the rakghoul virus?

After all something thwarted it getting off Taris and they haven't exactly recovered well since KOTOR!

The villain is a mad biologists named Isaac the plot is that he has been baiting ships and using the crew as test subjects with a distress signal he captures the pcs uses his latest strain of the virus on them they break out and and attempt to find him the pcs have one standard day before they transform into monsters allowing some tension. Isaac has the cure in case of an emergency so the goal of the pcs is two fold get the cure and survive escaping.

Sounds cool!

If you are looking to have a good amount of horror and mystery as opposed to horror-themed action, I think its important to build up to the reveal. A buddy of mine recently wrote a blog post on the topic: http://www.gnomestew.com/gming-advice/fear-itself/

Suggestion: Feel free to take some time building up the suspense and tension in the early stages of the adventure. Maybe when the PCs board the ship, the docking collar locks behind a heavy blast door automatically. The control panel is fried on this end, so they will need to go deeper into the ship to find the main computer.

The corridors of the ship are eerily lit in sporadic red emergency lighting. As they explore, they come along the grisly remains of previous spacers who fell into the trap, their bodies torn to pieces. Try and deflect their suspicions a bit with clues (remains, apocalyptic log entries from previous spacers, etc) towards other aliens, maybe even Rathtars so your PCs think you are taking a page from TFA. As they proceed further, start to drop some more specific hints towards Rakghouls like torn clothing and armour as if something has burst the attire from the inside. Maybe throw in a comic scare, with rustling from behind a panel which turns out to be innocuous Gizka. This bit of comedy can help enhance the horror.

Finally, the PCs come across a survivor. He's quite injured by vicous claws and is both sick and delirious. As the PCs question him, he rambles on about monsters and begs for them to take him with them. Suddenly, he hideously transforms into a Rakghoul and starts attacking. Cue transition to action horror!

Just a few ideas. I hope your game turns out awesome!