The Finder/WMG

Walter found the aliens all right...but they made sure he'd never tell anyone
...by making him one of them. He's still in his body, but he's totally under the control of the alien parasite they put in his head. Hodgins is one of them, too, though he's on decent terms with his parasite, and they came up with a way to end things that wouldn't seem completely out of character for Walter and cause suspicion. The mysterious Pope was one of them, though it's hard to say about the other guy, the one with the glasses. Jack and his slug pal are struggling because they're double agents and desperately want to find a way to get the word out but without being detected-which would get Jack a partner who wouldn't be as friendly as his current one. Oh, and the aliens are in the Jeffersonian too. Booth, Brennan and Cullen. (ok yes this troper is doing a Bones/Animorphs cross fic and this ep is amusing to try and work into it.)
 * No, no, no. They're Time Lords, obviously.

Walter was in the same Special Forces unit as Augie.
They can't meet EVER again because having someone with Walters compulsion in Langley gives the entire Seventh Floor panic attacks.