The mod story does not consider events in Half-Life 2:Episode 1. After explosion of citadel, G-man immerses Gordon Freeman in stasis, but after a while deduces it from there for the new mission. The target of this mission is penetration into a citadel which is in City 18 (the city located near to City 17). In this citadel there is a teleport in Combine world. Using this teleport, it is necessary to get in Combine World and to destroy their leader.
While it ends rather abruptly with little payoff, Penetration is an excellent Half-life 2 mod from the early days, with splendid pacing, design and gameplay.
Give this a gander, you won't be sorry :)