The Maria Mystery: Death

One of the greatest mysteries regarding Maria is how she died.

Sonic Adventure 2
Maria's "death" is shown twice.

• SA2 doesn't actually show Maria's death. While it would often be assumed that Maria was killed helping Shadow escape, it's not directly shown.
• Do to both limited technology and the need to censor gore, it's hard to tell if Maria already had been shot, as future appearances suggest, or if she was simply killed after Shadow already escaped. 
• Her death is confirmed by Professor Gerald's diary: "I found Maria's name among those who died."

Sonic Battle
-Sonic Battle also confirms her death on the Ark. It mentions her last words, leading to wonder who heard them and told the Professor (likely GUN rather than Shadow because it mentions "they told me").

Sonic X
Maria's "death" is shown three times.

-A scene similar to SA2 is shown in Shadow's flashback, where Maria falls at the end (her "fall" is partially censored in the English version).

-A scene nearly identical yet different was shown as recalled by the man who shot her. This confirms her as being shot releasing Shadow (after being warned not to).

-Maria is shown in a separate flashback, in a setting more akin to SA2, on the floor (presumably already shot), where she asks Shadow her promise.

Sonic X English Censorship possibility

-the man who shot Maria Mr. Schimtz mentions that Maria was "taken away," opening the possibility that Maria was still alive. However, this was also after the man erupted in tears saying "she was so young." It's possible Maria was injured and died later, or perhaps he was referring to her dead body.
-Ultimately, the show often used phrases such as "take away" in place of "kill," so it's likely she died one way or another.

Shadow the Hedgehog
Maria's "death" is shown three times.

-The first cutscene shows Maria shot in one of the Ark's halls. While the scene of the two fleeing had previously been in both SA2 and SX, this was the first time Maria was shown to be killed in the hallway.

-After "The Doom," a level set during GUN's massacre, Maria and Shadow run into one of GUN's robots. Maria then disappears and and image of her falling is shown. Maria was implied to have been killed by the robot.

-Maria is shown falling to the floor like in Sonic X, where she begs Shadow to save the world. She was presumably shot/injured right before this.

Shadow the Hedgehog Censorship

-When the game was planned to be rated Teen, the hall scene where short-haired Maria was shot was longer (but how/where she was shot remained).
-The scene where Black Doom "reminds" Shadow of what happened originally has Maria's death reflected in the hedgehog's eyes. Since the scene shows the Shadow and Maria running down the hall, it may have been another indication that she was hurt in the hallway.

Archie Comics

-Maria is shot helping Shadow escape. Although the style changed, the scene was the same.
-During one of Shadow's flashbacks in the rebooted continuity, Maria is shown with an expression similar to the hall scene of Shadow the Hedgehog. However, her hair is it's normal length, meaning it may have simply been a similar--but not the same--scene.

Conclusion

While mild compared to other genres, it is rare for a character to die (without returning) in the Sonic series. With the different plots and episodes, what happened can get confusing, but it's clear she died helping Shadow escape.

Was Maria killed before Shadow was released or in the hallway?

Maria was shot before Shadow was released and likely died after. The hall way scene was most likely a creation by Black Doom to cloud Shadow's judgement or corrupt his memory. "The Doom," the stage featuring GUN's take over, may be a pun. It describes the tense situation as well as who was creating the memory--Black Doom.

Who killed Maria?

A Gun Solider. In Sonic X this character was shown to be Mr. Schmitz (Mr. Smith in the original).

Notably Mr. Smith knew about Professor Robotnik's experiments and thought Maria was releasing multiple creatures. Mr. Schmitz only heard rumors and did not "know what to expect," and he thought there was just one creature being released. 

In the games the solider is hard to distinguish from other soldiers.

Why kill Maria?

As seen in Sonic X, Maria was sending a powerful, dangerous creature to Earth. Mr. Shmitz warned her to stop, stressing that he was serious, but Maria pulled the lever anyway. From his point of view, he had to fire (though he regrets it).

The games are a bit harsher, only saying that they "eliminated" everything related to the project. The professor mentions that they would all be imprisoned, but it's unknown if other survivors were incarcerated. "The Doom" level suggests that fellow researchers were harmed, if not killed. 

Maria also may have been targeted because of her connection to Shadow.

Is this the darkest point in the Sonic series? 

No. Ever hear of "Fun is Infinite?" Or Sonic 06: Last Story?

Maria's death would have a large impact on both Shadow and her grandfather Gerald Robonik. Robotnik went insane from the event, plotting to destroy the world he once tried to protect. Shadow began to set the mad man's plan in motion, but remembered Maria's true wish. He strives to keep her promise to this day.