I'm a little confused by the ending though…the log to me implies that U53 were destroyed by the 4000-1 instances.
Basically, Incident 4000-28 was SCP-4000-1's (nearly-completely-successful) attempt to take over Area-R01 and terminate all personnel using only -B instances. Here's a summary, as well as some clarification on events which weren't mentioned in the logs:
01:05 [R] BREACH ALERT! LOCKDOWN INITIATED!
01:05 [R] BROADCAST [from: lily_413@site64.foundation.scp]: CODE VIOLET!
01:05 [L] Internal API: Radio communication disabled by user (automated userscript alphabreak.sh).
Having suspected something like this was going to happen after the ultimatum the previous day, and knowing that 4000-1 likely had access to the PSHUD remote-override signals, U53-Lily had set up a script to automatically brick her own radio module when a breach alert triggers, thus making it impossible to receive remote-override signals in the first place. This was good because, soon after:
01:05 [M] Remote SSH Access Signal A received. Control transferred.
01:05 [F] Remote SSH Access Signal A received. Control transferred.
This was SCP-4000-1 using a remote-override signal to take control of U53-Mallow and U53-Fenn. At this point, -1 has control over the facility's computer systems, as well as 2/3 of Upsilon-53.
01:05 [R] API Error. Environmental control cannot be shut down by remote request. Incident logged for manual approval.
(this line is repeated 384 times)
01:06 [R] API Error. Atmospheric mixture cannot be modified by remote request. Incident logged for manual approval.
(this line is repeated 617 times)
01:06 [R] API Error. Exterior airlock doors cannot be opened by remote request. Incident logged for manual approval.
(this line is repeated 51 times)
4000-1 tries to take various steps to kill the humans in Area-R01 (shutting down environmental controls, modifying the atmospheric content, and opening the exterior airlock doors). Fortunately, the system won't allow obviously-fatal actions to be performed remotely.
01:06 [M] Movement actuator system: external access.
01:06 [F] Movement actuator system: external access.
Unfortunately, 4000-1 happens to have control over two Foundation personnel. Mallow and Fenn are sent off (Mallow to the environmental control room, Fenn to the exterior airlock). Lily, realizing that the rest of her task force has been taken over by -1, starts looking for them.
01:10 [R] ALERT! REGISTERED DAMAGE TO EXTERIOR AIRLOCK DOORS!
01:10 [R] SECURITY: USER fenn@site64.foundation.scp HAS PERFORMED A HOSTILE ACTION! DEPLOYING REMOTE DISRUPTION SIGNAL A!
01:10 [R] RDS-A cancelled by ▒▒▖▚▛░▌▏▏
01:11 [R] ALERT! CRITICAL DAMAGE TO EXTERIOR AIRLOCK DOORS!
01:11 [R] ENVIRONMENTAL ALERT! ATMOSPHERE COMPROMISED! LETHAL ATMOSPHERE IN 3 MINUTES!
U53-Fenn (controlled by 4000-1) arrives at the exterior airlock and begins to perform a "manual override," a complex process which likely involved a large metal pipe, heavy rock, or similar blunt tool. 4000-1 prevents the security system from doing anything about it, and Fenn breaks the door fairly quickly. Mars atmosphere starts leaking in, breathable atmosphere starts leaking out, and 4000-1 prevents the breach-protection systems from activating.
01:12 [R] ENVIRONMENTAL ALERT! ATMOSPHERE SEVERELY COMPROMISED! LETHAL ATMOSPHERE IN 2 MINUTES!
01:12 [L] Warning: Registered damage to external systems.
01:12 [F] Alert! Registered severe damage to external systems!
01:12 [F] Internal API Error: Remote communications module not responding. Possible hardware compromise.
01:12 [F] Alert! SSH session disconnected! Remote override lifted!
01:12 [R] User fenn@site64.foundation.scp: account disabled by ▒▒▖▚▛░▌▏▏
Lily arrives soon after Fenn disables the airlock. She is damaged, but she manages to overpower him and manually break his communications module, severing the connection. Unfortunately, the airlock is damaged irreparably. Lily goes back, toward the environmental control room where 4000-1 is still trying to use Mallow to override environmental-system lockouts.
01:13 [R] ENVIRONMENTAL ALERT! ATMOSPHERE CRITICALLY COMPROMISED! LETHAL ATMOSPHERE IN 1 MINUTE!
01:13 [L] Warning: Registered damage to external systems.
01:13 [L] Alert! Registered severe damage to external systems!
01:14 [M] Alert! Registered severe damage to external systems!
01:14 [R] ENVIRONMENTAL ALERT! ATMOSPHERE LETHALLY COMPROMISED!
01:14 [L] Internal API Error: Movement actuator module not responding. Possible hardware compromise.
01:14 [M] Internal API Error: Remote communications module not responding. Possible hardware compromise.
01:14 [M] Alert! SSH session disconnected! Remote override lifted!
01:14 [R] User mallow@site64.foundation.scp: account disabled by ▒▒▖▚▛░▌▏▏
Lily arrives and is just barely able to overpower Mallow, disabling her communications module and breaking the connection. In the process, Mallow damages Lily's movement systems, leaving her paralyzed. Also, by the time this is complete, the atmosphere throughout Area-R01 has become completely compromised. All still-living humans in the Area die from a lack of oxygen soon after, leaving U53 as the only Foundation personnel on-site.
Mallow, seeing the situation as lost and having only recently gained back control of her body, picks up the paralyzed Lily and carries her to the remains of the airlock. They and Fenn take a portable communication device meant for Martian surface missions, leave, and activate a manual breach alarm on the exterior of the facility to throw it into a lockdown which -1 cannot remotely override.
01:21 [R] ALERT: MANUAL-OVERRIDE BREACH ALERT TRIGGERED! LOCKDOWN IN EFFECT!
01:21 [R] API Error. Manual-override breach alert cannot be disabled remotely.
(this line repeats 11,526,380 times)
4000-1 can almost certainly break through the lockdown. Why it hasn't done so, and why it hasn't simply retrocausal-ed Area-R01/MTF U-53/the Foundation in general, is a subject for a future tale.
This has been SCPDeclassified That is, essentially, what happened in the ending. If there's still anything that needs clarification, please feel free to let me know.