The substance is stolen from a government freight train using the Jetpack, which was stolen in the previous mission Black Project. The Green Goo is discussed very little and it is not revealed what it actually is. Since it came from Area 69, the green goo is believed to have something to do with aliens. The fact that it is securely protected by government officials, with no clues even given by The Truth, says that it may be a very valuable top-secret substance. Either way, The Truth seems to show a lot of interest in the strange substance. After the mission Carl gives the Goo to The Truth and that is the last it is ever seen. Where The Truth took the goo is unknown, though it could be where he resides in Leafy Hollow, Flint County, or Verdant Meadows as it is the last place we see it. There are various fan theories that the Green Goo has a chance of spawning in Area 69 after the mission. Many fan made Mods also use the Green Goo as a common trope.
The Green Goo itself is housed in a large clear vial with what appears to be some sort of tubular metal cage around it, possibly for protection purposes. The goo gives off a green lens flare.
Also, The Truth calls into the WCTR show Area 53 and talks about various conspiracy-themed topics. He states on the second time he calls, that he has held them (aliens) in my own hands. The aliens he may be speaking about may possibly be the Green Goo.