Answer: Raccoon
Elliott stayed out, on Halloween night, and tried to get the device to work to call for a spaceship to pick up E.T. It appeared as if the device did not work and Elliott told E.T. that he could take care of him and nobody would ever hurt him. In Elliott's next scene, he arrived back home, right as Mary filed a report that he had gone missing. Elliott told Michael that E.T. was all alone, in the forest, and he had to find him. Michael assured Elliott he would locate E.T. and bring him back home. Michael rode his bike, into the forest, and encountered him down by the creek. When he got to E.T. you could clearly see a raccoon, right next to E.T.'s body, since the animal had rings around its eyes. Michael scared the raccoon away and brought E.T. back home.