I would definitely encourage the players to spend a few minutes joking around and bragging about their character's exploits en route to the ship. Maybe even create a clear chain of command among the player characters. Perhaps you could play the group's Commanding Officer or give the title to one of your players to encourage RP. Anything to make the characters relatable and thus increase the drama once the horror begins.
I am not too well initiated in the Halo universe, but I do distinctly remember the Flood-centric levels of Halo 2. I imagine the sheer mass of Flood would interfere with communication and sophisticated electronics - let the players have their fancy gadgets and stay in constant contact for a while, but slowly and surely rip it away from them.
If I recall correctly, Master Chief is something of an outlier in the Halo World, not really representative of what the average soldier is capable of. Definitely play up the encroaching mass of Flood, the futility of the players' soldiers to fight against it. One Flood dies, nine take its place and a tenth one devours the corpse.
The objective for this scenario should probably be to simply survive. Maybe create a map of the ship and determine what might occur in the various rooms and hallways. Then allow the players to roam around.
As for personal projects, I am currently working on two campaigns: a Gamma World campaign drawing inspiration from Homestuck (see my avatar/mspaintadventures.com) and a CthulhuTech Migou campaign. The latter is really still in the gestation stage, because as much as I love the Mi-Go/Migou, determining any objectives for them beyond "SCOUR THE EARTH RAWR" is pretty difficult. Maybe a game that takes place during the initial invasion of the Migou?
My Gamma World campaign is almost ready, though. The players begin as mutants in Californee, a region that comprises one-third of the Untied States of Amereeka (the other two regions being Flyover and York). They are the leaders of a small tribe of nomads venturing northwards, battling mutated pigs and raccoons and moths and stuff as they go. Eventually, the players reach what was once Seattle and the suburbs surrounding it. Though the vast majority of the suburbs are marked with craters, there exists one house in absolute pristine condition. Perfectly intact, healthy grass and plants, even the mailbox remains standing. Basically, a picturesque two-story house from today's suburbs.
Then the players discover a child inside the house, forced into a kind of stasis for over 150 years. They notice the child remains seated in front of an Ancient (both figuratively and literally) computer, which is still somehow recieving electricity. The players activate the computer, and then the fun begins. The child exits the stasis, is floored by the awesomeness of the player characters (he has a fondness for really bad science fiction movies, as evidenced by the posters in his room), and asks for their help. He had intended to begin playing a computer game with his friends mere moments after the Big Mistake began, a game that would strip the Earth bare and create a new one in its place. What new planet will be created is up to the players, the child, and the child's friends, who are scattered across Amereeka (with one at a small Pacific island - radioactive sea adventures ahoy?).
My real concern is that this might be too railroady. I definitely want the players to have some motivation to follow through on the journey, or at least experience enough curiousity to investigate the frigging house. Not to mention the following events are quite hectic and delineate a pretty clear path for the players to follow.
