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Isaac is the original captain of the spaceship who was killed when Bradley raided the ship after Rylan disabled the ships weapons and defences. 

Isaac's body was then dumped in space and abandoned.

It may take more than a few searches of space before his body is found, depending what progress you have made in the game.

You will eventually find Isaac in space and when you bring him back to the ship, put in in the infirmary.  It took more than a few days for Arthur the scientist to bring him back to life, be patient as for me Isaac took approximately a week to return to life.

Did you gather all the materials the scientist needed, such as the Hibiscus Essence etc. and allow the scientist to do ALL his experiments with the materials. 

There are 3 or 4 experiments/test that Arthur has to perform with the HIbiscus Essence and they tests MUST be fully completed. Be sure to check they are full performed and that you talk to Arthur and get the research results. 

It takes a few days for Arthur to learn a little more about their properties and discover he needs to learn even more about the magical aspect of the materials, this means he will have to go to Harmonia.

At  Harmonia Arthur must  speak to Gabriel and learn more about magic and science, by doing this he learns how to improve his medical serums potency and finally restore Isaac to life.

But be very patient the serums only act slowly because Isaacs's body was badly degraded by being space for so long.