Dark Heresy, Deathwatch and Only War are all mission-based games to some extent, while Black Crusade has the characters making a dash for Daemonhood. But what about Rogue Trader? I couldn't really find anything about this, so what is its goal? Getting rich or die trying? Becoming powerful enough for the party to run a part of the galaxy on their own (with the Emperor's blessing, of course), or just hitting an X amount of resources?
Let's see. In Rogue Trader players are exceptionally powerful merchants with a Warrant of Trade that allows them to explore the unknown, exploit worlds, buy and sell extraordinary raw materials and powerful devices, as weapons. So, it seems that the primary goal is:
Well, not only cash, also power, contracts, devices, space ships. You know, your little merchant empire. Or, like the game says on its introduction:
Vast fortunes await on the edges of the galaxy, if you and your fellow Explorers can muster the courage to find and claim them. Renown and riches reward the bold, but the unwary find only anonymous deaths. A Rogue Trader who can wrest profits from a dangerous universe through luck, cunning, or sheer force of will enjoys something few humans in the 41st Millennium even know—a life of adventure and true freedom.
In game terms, all the money, power, contacts, allies and resources are represented by the party stat Profit Factor. So, if you want to think in those game terms, the primary goal of the game would be to increase the Profit Factor value.
Of course in a RPG characters can usually have the objectives they want. One of the most common would be glory, as Rogue Traders usually come from a family and they want to honour it. They can travel where no man in the empire have never been, so they can make a name in history.
Apart from those, rest of objectives depends on the characters. For instance, a template character is the missionary. For that character bringing the faith of the Emperor to outer men world, or attack xenos creatures can be logical objectives.
So what I'm doing in a RT game right now is I had them adopted by a powerful dynasty, the leader (of the dynasty) dies shortly afterward, gives out 'keys' to various former associates and rivals. They're goal is to reunite the dynasty (if they want to). Looking into some of the random generation tools out there is a good way to start, they take a good load off of a new GM to the game and can help form a starting point for an adventure.