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The crew can be instructed to research advances in ships systems (such as increasing shield strength) or in defeating Empire technology (such as decrypting transmissions or making weapons more effective against certain races). Science officers from the virtual crew can be assigned individually to each project. Science officers not assigned to a specific project split their contributions among all running projects. 

It is up to the command officers to guide this research. Before ships systems can be upgraded (by the engineering teams), they first have to be researched. So if the decision is to upgrade the shield strength, the science officers have to first research Shield Upgrade I. Once the research is complete, Shield Upgrade I will then become an upgrade option for each engineering team on any of the shield systems.

By training a large portion of your crew as Science officers you will be able to research technologies faster, but at the cost of having fewer engineering/medical/security personnel.

Research projects for defeating Empire technology become available as you encounter each race. For example: After you encounter a Hibernian ship, the following research projects may become available.

- Decrypt Hibernian non-secure transmissions
- Decrypt Hibernian secure transmissions
- Decrpyt Hibernian top secret transmissions
- Investigate Hibernian shield vulnerabilities for weapons
- Investigate Hibernian shield vulnerabilities for transporters
- Investigate Hibernian sub-systems for specific targeting
- Investigate Hibernian warp signature for longer range identification
- Investigate Hibernian weapons to improve Federation shielding
- Investigate Hibernian impulse engines to improve Federation target lock
- Investigate Hibernian society to improve diplomacy
- Investigate Hibernian combat tactics to assist with close quarter combat


Each topic of research has a percentage chance of being completed each hour (based on the number of science officers working on it and the complexity of the task). This is to reflect real life research. There are no guarantees that simple research will be completed within a short time frame, and no guarantees that more complex research will be completed at all.

Certain upgrades to ships components (such as re-purposing rooms as science labs) provide a boost to the ships research capabilities. In addition, external research stations can be constructed by the engineering teams. These stay in fixed areas of space and provide a boost to the parent ship at all times (as long as they are manned by crew members).