Summary

In short...
The players play as terminally ill people (canonically these people) that have had jobs at one or more of the best science and military corporations in the world, known as the Prime Sevens. All financed by the Council of the Order of Menace (aka the "Illemonati").

The Prime Sevens are: All held in check by earth's secret private mercenary defence force: the Sven Co-op Institute (huge paramilitary force, which oversees global security and looks over the prime sevens).
 * 1) The 3 mesas: Black Mesa, Yellow Mesa, Momma Mesa
 * 2) The 3 corpos: Aperture Science, Merkwurdig Labs, Bodermart Express
 * 3) And the Team Fortress Industries.

The players are offered a chance to survive certain death through an experiment with chumtoads if they accept being recruited as property of Sven Co-op. The hidden truth is the experiment has a 99% chance of failure, but the players end up surviving and wake up years later during the attack of the traitors lead by Richard Boderman, while now the experiment has given the players the power of respawning which makes them immortal.

With this new power (unable to be reproduced even though scientists tried with catastrophic results) the players start a very long journey under the command of Sven Viking, leader at Sven Co-op. They save the world in several occasions: from Boderman, the illemonati, the reptilian empire, terrorists, ninjas, metal gears, the old gods, alien experiments... until the mysterious GMan arrives and is found guilty of many of the previous problems mentioned, and more to come. Aliens start to appear more commonly as his presence advances.

GMan gathers armies from everywhere and creates chaos with shady deals that tip the balance of the world clashing with the most dangerous factions and questionable technology. With only Sven Co-op and the players at the helm to solve the problems (with bullets), finally right when GMan is about to be captured (little did they know who he was or what he was capable of) the Black Mesa incident happens and all hell breaks lose without control.

Attempts to contain the invasion fail over and over until its too late. The military make things harder, but key members of Black Mesa are rescued. The GMan resurrects Sven Co-op's enemies to destroy their HQ to make sure they don't interfere, and the players are left adrift alone right after Black Mesa is nuked and the portal storms begin.

With a small team of survivors, the players try to fight against the invading Universal Union, but the new plan also fails and sends the players 10 years into the future where the Combine now rule the world. The players are given 3 nukes to detonate and destroy the main Combine machinery and defeat the Consul.

This catches the attention of the GMan who admits failing for not realising about the players' powers until that moment, and after a quick testing of their abilities, and making them fight Adrian Shephard (effectively replacing him with the players), the GMan recruits the players. But the unthinkable happens, one of his employers intervenes before GMan takes the players away, and breaks his old contract, creating a new one and thus now becoming allies, leaving the players alone so they can finish their original mission.

The players destroy the combine dome, the air exchange and the citadel after defeating the Consul, although effectively chain detonating the citadels of all of North America, wiping it from the map.

GMan then takes them back in time to clean up Black Mesa East so Odessa and Eli Vance are able to start the resistance. And fast forward in time to help Odessa and Tor take Freeman's HEV suit to Kleiner's lab. And even more into the future to protect Alyx with the help of Father Grigori and Annabelle right while Ravenholm is being shell'd. This all to pave the way for Freeman to arrive at the right moment. Yet then once again they go to Ravenholm to help Shephard and Father Grigori in his last moments after the fall of the Citadel 17.

And then, the final piece, to help GMan get the Source(tm) created where all time and space collides: The Borealis. But the employers finally find out about this treason and intervene sending the Source to the void and capturing the players to do their bidding.

The players are tested for loyalty and eventually fight through time and space under their gaze, passing hands through several different GMen and other creatures acting as their envoys. Until their job is done and the players are sent to a dimensional prison. Which they eventually break from with the help of GMan and the last reptilians who want to avenge Earth, and a mysterious scroll that speaks and guides them.

The players have to take the long route to recover the Source through different crazy dimensions, and finally after they get it, they have to use it to get out of the void where it fell. This throws them right to where everything begins: the Valve Intro.

The employers are there (Mr. Steam, Mr. Valve and Mr. Gearbox). Mr. Gearbox reveals himself as the rebel that helped the players and broke GMan's contract, sacrificing himself to defeat one of the other employers. GMan brings the entire cavalry with him: Freeman and the Vortigaunts, Prospero's Librarian, Barney, Chell, Mel and Alyx with the LAW (Leather Armor World Resistance Force), and with the power of the Source they attempt to defeat Mr. Steam, but to no avail, he is too powerful. At the last moment Alyx is the only one left standing and attempts to destroy the Source with Gordon's crowbar. But the Source cannot be destroyed because it is guarded jealously by Lord Gaben who arrives to defend his dollar income, stopping time and destroying everyone present except the players.

The players can only watch without a spawn point to respawn, but Mr. Steam realises he was just a pawn in Gaben's game and so he betrays his creator before he is deleted, giving the power of Source to the players so they can fight Gaben to give Half-Life an ending.

Lord Gaben is too powerful, but a miracle happens... the messiah Marc Laidlaw appears and gives the players the means to an end that nobody wanted: to let his dream go. For this he gives the players the deadliest weapon ever created: the "Carve Tool", to destroy the fabric of reality.

The players do not defeat Gaben, but they destroy the entire Half-Life franchise, giving it a bittersweet ending.

But while everyone is suspended in nothingness, Gaben is eventually swayed by the community's efforts, and so he decides to give Half-Life a second chance. The entire franchise is getting ready to be reset. He sends the players back to life in a new alternate reality and timeline, where they are being expected by the All Seeing Vortigaunt and his squad.

Now with the players' characters gone, they are just pure Source energy, and avatars of themselves. They are tasked to help imprison GMan, for which they sacrifice their Source energy powers and their vortigaunt friends to do so. Only to after find out they are now part of the game itself again, reappearing when needed anywhere, for as long as they are needed, to fix events in the franchise.

And so, they reappear right after Alyx was recruited and mind wiped by GMan, right after Half-Life: Alyx's events. They take unconscious Alyx to safety from the prison's wreckage to Black Mesa East in the canals where the All Seeing Vortigaunt is waiting, only to then fade to non-existance again... Until they are needed once more.