It leads to the shower room. Choosing Door 3 will always lead to the Sub Ending since the player is forced to go through Door 2 after (except in the iOS version where Door 3 leads to the Syringe Ending).
After an unsuccessful search for Snake, everyone regroups and decides to move forward. Lotus proposes to leave one member behind, due their digital roots making it impossible for all 7 of them to pass through. Ace volunteers to stay behind, injecting himself with Soporil so that everyone is forced to leave him behind despite their objections. It is later revealed that he did this to prevent anyone from going through Door 3 and seeing "Snake's" corpse.
That decided, the group of 6 were left to choose which door they wished to enter. The initial plan was to take Door 7 and 8, but it would force Junpei to be separate from June. Not wanting that, he decides to force them to let him take Door 3.
To enter Door 3, Junpei had to trick the other members of the group. He first implies that he had found a way for them all to escape, and asks Seven and June to verify their numbers before doing so himself.
7+6+5 = 18, 1+8 = 9
Now, only an additional digital root of 3 is required in order to enter Door 3. This leaves only two possibilities: either Santa (7+6+5+3 = 21, 2+1 = 3) or Lotus and Clover (7+6+5+8+4 = 30, 3+0 = 3) could join those who had already verified. Junpei chose this point to explain this very fact to the others and lays his hand on the RED's lever, effectively forcing them into a race for survival.
Santa manages to outrun Lotus and Clover despite them having an advantageous starting position. He also is fueled by his desire keep his and June's true bracelet number hidden in the process. If Lotus and Clover scanned their bracelets, Door 3 wouldn't open. This would raise the question as to why and possibly cause their secret to be revealed.
7+6+5+3 = 21 = 2+1 = 3
Junpei then pushes down the lever while receiving hateful glares from Lotus and Clover.
Behind Door 3
Upon entering, the DEAD is nowhere to be found. A quick investigation reveals that most of the path is blocked by thick iron plates, leaving only a rusty iron door accessible. This door leads to the shower room, where the DEAD and the terrible stench of death is located.