I had an idea about one day running something where the Explorers come across either a wrecked station or ship. Auspex tells them there is a faint power source still active. On investigating they find lots of blown out/open to vac corridors - done by explosive charges placed on the doors. Eventually making it into an area that still has pressure they find a *crap* load of alien corpses and a Space marine missing an arm and a leg and in suspended animation due to the damage.

Assuming they recover the body, on plugging it in the armour gives some sort of coded message/advanced imperial distress message, etc.

If the Explorers track down the Marines Chapter (One whole arc?), there is a tense standoff until they can state their case, then they are boarded (without violence) and go through the whole 'meet people, be refused leave to depart'. A few weeks later they get to meet the rescued Marine, complete with new bionics.

He was part of another expedition that has long since vanished into the Expanse, wishes to try and find them, is given leave to depart with the Explorers…

     What my Gm did is our Flag ship was sucked into the Warp and then spat out in the Processional of the Damned. We then proceeded to ram into a derelict Space Marine Battlebarge of the Red Skulls chapter. Turns out, the Red Skulls had been wiped out a few hundred years ago, so the 3 Terminators on board are the only left alive. They then, asked(with guns pointed at our faces and a swarm of dead murder servitors surrounding them) that we take them and some "special cargo" back to Imperial Space. Basically, we took the 3 Terminators, and about 500 Red Skulls geneseed to an area of space that we where able to transfer them to the Inquisition.

     We didn't ask any favors of them, but something like this could be a base for more friendly relations that could lead to them assisting us, or our Dynasty, in the futre

Off the top of my head, a scenario that could work for what got you the alliance could be something like:

Raven Gaurd units were cut off and trapped behind enemy lines. Imperial forces were unable to move in to support. The rogue trader broke through to them, helped them accomplish thier objective and escaped with them, returning them to their chapter.

Generally I would say any sort of suitably heroic action that the rogue trader does to help the space marine chapter in question could qualify for what began their friendly association. But only if it is something the RT was not actually obligated to do, would have to be above and beyond the call of duty, and heroic both in my opinion.

I was in a mixed RT/DW campaign that began during the Great Crusade. A well equipped rogue trader vessel with no less than three full squads of marines from different legions (each led by the space marine PCs). Some great rp with tensions between the SM factions, and between them and the mortals.

A 40k rogue trader game can accomodate space marines but there needs to be solid reasons why a space marine (or marines) are on board. They will also attract attention if they act publically (perhaps against the desires of the rogue trader) which could lead to all sorts of fun consequences. Chapters can easily have their own goals that do not align well with the rogue trader's!