As "G-Man" required you to work for his agency, you refused and you found yourselves teleported within a broad arena where tons of aliens awaited you to make you pay the note for all that you had made them with them like with their chief, Nihilanth. Against any waiting and after a hard battle, you succeeded in overcoming and of the scientists of Black Mesa made a success of with you teleporting you back to Earth where they placed you in a tube of care filled of a proteinic and nutritional liquid to keep you in life.
While you recovered your wounds, G-Man, with governmental approval, sent many soldiers on Xen to carry out a fast invasion and three respectively named military bases X1, X2 and X3 were built to take the control of planet and to hold the aliens in respect. At the beginning of this deployment of forces, the task seemed easy and the opposition alien remained tiny. But this apparent lack of aggressiveness hid in fact the preparation of a great counter-strike which quickly swept the defenses military and put the three human bases in a bad shape.
Facing this military disaster, G-Man decided to return to Earth in the search of a missile equipped with an enormous nuclear warhead and to send it to Xen in the idea of getting rid of the alien threat. Obviously, he considered that it was to be the only way of preventing the aliens from carrying out a new invasion on Earth.
During this time, a team of scientists furtively teleported on Xen discovered that another peaceful alien species living on this planet had a technological advance of several thousands human scientists. The assistance of these new aliens friends would be of a great help for humanity. Then, when the scientists returned to Earth and discovered what G-Man have planned, they could find only one person able to counter the plans of G-Man... You!
Now, you must neutralize the missile and prevent the government from destroying Xen and your new friends. To achieve this mission, you will be teleported in a military base close to a deposit of nuclear weapons. You will have to escape from the base and penetrate in the deposit. Once you fullfilled your job successfully, the scientists will teleport you back ...
At least, you hope for it...