SCP-682 is pursuing after D-9341.
The Hard to Destroy Reptile has a supreme hatred of humanity and wants nothing more than to destroy us all. Whatever it consumes it absorbs into its very being. Becoming more deadly with whatever or whoever it devours. The Foundation however, keeps stopping its plan, re-containing it every time. As for Benjamin, before he was demoted to D-class, he meddled with the anomalous phenomena dubbed the "Spiral Gestalt". He can now relive any task over and over until he achieves the best possible outcome in every scenario. 682 is working with the computer AI SCP-079, having a length conservation. The computer really wants Benjamin to go to Gate B, where the giant monster breaks out. Should he try to read the documents on The Hard to Destroy Reptile, the AI will kill him there and then. Although both endings where D-9341 gets further away from the complex, SCP-682 escapes just after you, regardless. The Foundation again, interfere. But if SCP-682 should ever succeed in consuming the former researcher, it will acquire precognition to overcome any threat, to thwart and counter every attempt the Foundation has to re-capture it, 682 would become a true death god, and humanity's days are numbered... D-9341 is an SCP, but not Born Lucky.
His actual ability is to reload from saves, Undertale-style, which is why they think he's Born Lucky. He's actually reloading.- This would make him have Retroactive Precognition. This Youtuber theorizes the same thing: https://www.youtube.com/watch?v=TN1eue2AcMA
basically saying that his ability to know what's coming and how to operate things he should have no knowledge of, stems from the research that got him demoted from a Class 4 Researcher to a Class D test subject: The Spiral Gestalt. He apparently completed his research or at least got part-way into it. Enough for him to "see" every possibility and outcome; or to try those outcomes, fail, and these memories are then sent to every other version of D-9341; or that he has linked himself to YOU, the player, as the medium to transfer these memories.
The facility was actually a disposal site created by the Chaos Insurgency.
The facility seen in the game was never meant to actually contain the SCPs stored there, instead it was meant as a place where dangerous SCPs could be gathered and destroyed. The Chaos Insurgency manipulated the Foundation to create the facility. One of their operatives, Dr. Maynard, was even the chief designer of the facility, especially its modular design (which made it harder to navigate, thus contain a breach). This would have included the nuclear destruction failsafes. Dr. Maynard had several SCP that were a threat to humanity, including SCP-079, SCP-106, and SCP-682 (among others), stored in the facility. Dr. Maynard then had a fellow CI operative, Agent Skinner, assigned as part of a 2 man team to guard SCP-106's containment chamber. Once Agent Skinner's Foundation assigned partner was distracted, he released SCP-106. SCP-106 started abducting staff members of the facility. While the rest of the staff was distracted trying to recontain SCP-106, Dr. Maynard entered SCP-079's containment chamber and gave him access to the facility's networks (presumedly among other acts of sabotage like breaking SCP-012's containment apparatus). While SCP-106 was able to be recontained, SCP-079 soon afterwards used his network access to cause containment breaches across the facility. The plan was to cause a large enough containment breach that the Foundation would be forced to activate the failsafes and nuke the facility, thus destroying all those dangerous SCP (or so they hoped).SCP-106 hates weed
Which explains why he sometimes spawns in the head office, the only place you can get 420-J. He doesn't want people getting high, as there's "better stuff" according to him.