The Voyager has one of the most complicated chain of requirements to get all its loot. Scopely released the graphic below to help you follow what you have to do.
So basically you kill Hirogen Hostiles to get relics, which get you the mats you need to summon 8472 hostiles, whose loot lets you get Voyager travel tokens for the Voyager to mine Common and Rare Anomoly Samples, which get turned in for more loot.
In the refinery, you have access to ship parts for normal ships, the Amalgam, the Cerritos, the Franklin-A and the D'vor Feesha. This is by far the quickest way to get 4* and 5* ship parts.
There is a Silver Blood Voyager flying around the Delta Quadrant. To find it, you just use the summon ability like you normally would, and it has a chance of being summoned if it's in the system. Eventually you'll probably encounter it. When you do and kill it, you'll get a chest that pops up eventually in the Voyager refinery.