Anticlimax Boss: The last part of the second game, sadly. Not only there's Volkov in the wheelchair (see Villain Decay), but the very last enemy you have to confront is just a Giant Mook, maybe a little more resistant than the others, but he doesn't even get an energy bar. Even Isako may qualify; the second and last encounter with this boss is almost boring, compared to the battle inside the tornado in Ohio.
Crowning Music of Awesome: The main theme of the first game. The theme of the second game, while good, is not at the same level, but you can hear the first theme during the ending credits.
Germans Love David Hasselhoff: The first game was quite successful in Germany, thanks to many positive reviews in the German gaming press, and probably also to its taking place in several German locations. So much that, while the first edition had only translated subtitles, the local publisher took the effort to also dub the game for the GOTY rerelease.
Sequelitis: Contract J.A.C.K. was done by Monolith as a side project to give the artists and level designers something to do while the programming team was working on building the LithTech Jupiter EX engine that would later be used as the basis for First Encounter Assault Recon. The lack of concentrated effort was reflected in the quality, and the franchise got canned because of it.
Tear Jerker: An unexpected one at the end of the second episode. "Abigail..."
Curiously, at first there seems to be a Retcon, since you assume Volkov's condition is due to his fall in the icy pit near the end of the first episode, apparently ignoring the very last scene of the same game with him in perfect shape, meeting the Director. You also might end up assuming that his first meeting with King Pierre as well as a letter you can find towards the end of the second episode, where he claims he got injured in a skiing accident while on vacation, is a justification he gives to cover his failure. Then, at the end of Contract J.A.C.K. you find out that it's all true.