Rogue Contracts are agreements between bounty hunters and notable organizations, namely the galactic federation. Usually these contracts involve the assassination or destruction of the target, however gathering information and even rescue missions have all been legitimate contracts in the series history.
Notable Examples by game
In Metroid (and in extension, Zero Mission and Prime Pinball), after failing to destroy the space pirates base, and with fear of an outbreak of Metroids, they hire bounty hunter Samus Aran to infiltrate the base, destroy mother brain, and kill off all the metroids.
In Metroid Fusion Samus is sent to SR388 to protect a group of Biologic Space Labs Research Station employees who are studying the planet's life-forms. After being infected by an X-parasite and saved via the metroid vaccine, she is sent back by the Galactic Federation to investigate the aftermath, and subsequently destroy the X-parasite on the planet.
In Metroid Prime 2, which takes place between the original and Fusion, Samus is sent to investigate Aether after the disapperence of the G.F.S. Tyr and its crew of 22. Her mission is to find them and to protect any survivors.
In Metroid Prime Hunters (shortly before Prime 2), the galactic federation intercepts a cryptic message about an "Ultimate Power" ("The secret to ULTIMATE POWER lies in the ALIMBIC CLUSTER."). They send Samus Aran to obtain it and give it to them, or destroy it if nessesary.
In Metroid Prime 3 (6 months after Prime 2), after being informed of a Phazon-Corrupting virus, Samus (and other bounty hunters) are sent to deliver this vaccine to other members of the federation. However, before they can begin their mission, they are attacked by a squad of space pirates, and they first protect the federation, however Samus is infected with Phazon, which actually has many fighting benefits. She is informed she must complete the missions of the other now missing bounty hunters, as well as learn of their wearabouts.