35 minutes into Chuck vs The Subway (season 3, episode 18) Daniel Shaw shoots Stephen "Orion" Bartowski in the chest, to interfere with Chuck's emotions thus preventing his Intersect from functioning.

To those who watch Chuck for unimportant things, such as romance, this is a non-event. For those who watch for the content that is actually interesting, such as the spy stuff, the death of the world's most ecentric computer genius is a devastating blow.

To think that the man who began as the mysterious creator of the Intersect, introduced to us by a flash consisting entirely of redacted information and in his first onscreen appearance escapes from Fulcrum by blowing up an apartment block by remotely hijacking a predator drone, was dead. Season 4 will be rather empty knowing that there will not be any surprise appearances of Orion.

Well it would be, if he was actually dead.

There are many clues and hints which indicate that Orion is not dead, or at the very worst, did die but will still be revealed to be alive in season 4.

The living dead

The first person to come back to life in Chuck was Bryce Larkin in season one, who was resurrected by Fulcrum after being shot in the chest by John Casey. Bryce is then shown to die as his computer short-circuits. During a flashback in Nemesis Tommy tells Bryce that if he does not tell him where the Intersect is he will let him die again.

In Predator Vincent is caught in the explosion caused by Orion's predator drone destroying the apartment block, he is later revealed to have survived and is later shot in the chest by John Casey. Vincent swallows blowfish poison to ensure he dies. He is later revealed to have survived both being shot in the chest and swallowing the poison. He explains Fulcrum agents are trained to withstand the effects of the poison. Obviously after blowfish poison and hellfire missiles, bullets are secondary.

Daniel Shaw is shot in the chest in Other Guy. The Intersect's malfunctions in Tooth hint that he is still alive. At the end of Living Dead Daniel Shaw is shown uploading an Intersect.

Additonally, the majority of Fulcrum and Ring agents Chuck flashes on are shown to be presumed dead or killed in action.

Given the large number of people in Chuck who are supposed to be dead, but are still alive, as well as the number of people who are explicitly shot in the chest and were bought back to life, there is a large possibility that Orion is still alive.

"... when you're dead in the "Chuck" universe, there's a tendency to not be dead ..." ~ Chris Fedak

In addition to the above, Orion himself has died and come back to life once already.

Near the end of Predator Orion is captured by Fulcrum and taken onto a Helicopter. His Predator drone begins a security sequence and fires a Hellfire missile at the Helicopter, vaporising it. In Dream Job Chuck's dad reveals that he is Orion after he uses his signature wrist-computer to shut a door close on Vincent (who had, once again, survived being shot by Casey at the end of Predator).

"... Dad, I saw you die. I saw you explode in a Helicopter." ~ Chuck, Dream Job (S02 E19), 32:28

"I see how I could have given you that impression. I've had to die quite a few times, one of the perils of being Orion." ~ Stephen Bartowski, Dream Job (S02 E19), 32:34

Necessary for the plot

The writers in Chuck are not afraid to get the series into a tangled mess of plot twists and drastic changes before pushing the big reset button and setting everything back to how it was, as the plot dictates it. Consider the end of season 2 where Chuck, Casey and Morgan have quit the Buy More. Morgan is going to Hawaii and Chuck is going to do "whatever [he] wants". In the first episode of season 3, Chuck, Casey and Morgan are back working at the Buy More.

This is done again in season 3, Casey loses his job at the NSA. This is necessary to enable Casey to kill the mole Chuck was supposed to and to provide a reason to keep this information from Sarah. Later on Casey is given a full-reinstatment with his old rank back.

If the writers are willing to make such dramatic changes and then reset them to provide fuel for a few guilt-tripping, angsty episodes killing people as the plot dictates and then bringing them back whenever it suits is not a long stretch.

Orion's death in Subway is necessary to give Shaw a means to prevent Chuck's Intersect from functioning and to give Chuck only one possible choice going forward. With his own Governor stolen by Shaw and the only known person capable of making a Governor dead, Chuck is left with no option but to chase Shaw to get the Governor back. Without this plot-twist Chuck and friends could have left, gone into hiding and left The Ring to take over the Government.

Foreshadowing or coincidence

Along with the direct quote from Orion about how he has had to die "quite a few times" there is obvious foreshadowing mere minutes before Orion is shot. It would be a rather large coincidence that Chuck and Orion should discover the Ring base where Shaw was resurrected and uploaded with the Intersect, given that it contributes very little to the plot; since Chuck already knows that Shaw is alive and has an Intersect, finding this place means nothing. Other than to give an obvious clue to the viewer that when Orion is 'killed' less than five minutes later he could be ressurrected just as Shaw was.

Season 4

Orion's death was an essential component is setting the stage for season 4. As he is dead he was unable to stop his email being sent to Chuck giving him details of his secret base and the work he has been doing for the last 20 years. There will obviously be many things that Chuck and friends will need to discover which Orion could have told them if they knew he was alive. The question is who will bring him back to life; The Government, they could put the world's best computer scientist to good use. The Ring or another evil organisation; they could use him to build a fullscale Intersect or something even better. Or perhaps even Team Bartowski, after they locate their mother they could ressurect their dad for a full family reunion.

Post finale update

The series finale of Chuck came and went without a return from Orion. Some will say he was dead and the ressurection lab can only be used by bad guys. Some will say he is still alive but never appeared on camera, just like how we can assume Sarah got her memories back, and some will say those people are delusional, then there will be a big debate about it concluding with lots of people getting angry over a TV show. Whatever you say, maybe there will be a movie.