This complete Forensic M.E. Protocol Case 3 walkthrough provides the full solution for 'The Seraphim Cipher,' guiding you through every puzzle and evidence location needed to achieve the S-rank true ending. Unlike other guides, we'll cover not just the critical path but also the optional evidence required to unlock the case's best outcome and associated achievements.
The primary objective of Case 3 is to solve the murder of Dr. Aris Thorne, a lead researcher at the powerful Aethelred Biotics corporation. The investigation quickly reveals a conspiracy involving corporate espionage, a hidden project codenamed 'Seraphim', and a traitor inside the company. To get the S-rank, you must correctly identify the murderer, expose the conspiracy, and present a flawless case using all available evidence.
Initial Crime Scene: Dr. Thorne's Lab
Your investigation begins in the victim's laboratory, a chaotic scene of smashed equipment and scattered research notes. Your first priority is to perform a full M.E. (Memory Extraction) scan on Dr. Thorne and secure the obvious physical evidence.
Analyzing the Body (M.E. Scan)
Interact with Dr. Thorne's body to initiate the M.E. scan. This is a timed sequence where you must stabilize the memory fragments. The key is to sync the pulse frequency to the on-screen wavelength. You'll get three critical memory fragments:
- Fragment 01: Dr. Thorne arguing with Director Valerius about project funding.
- Fragment 02: Thorne frantically typing at his terminal, mentioning a "failsafe."
- Fragment 03: A distorted image of someone shattering his datapad.
Successfully scanning all three adds [Evidence] M.E. Scan: Thorne's Last Moments to your case file.
Locating the Initial 4 Evidence Pieces
After the scan, you can investigate the lab. Four key pieces of evidence are here. Don't leave until you have all of them.
- [Evidence] Overturned Beaker: On the floor near the main console. A simple scan reveals a neurotoxin residue, which becomes your cause of death.
- [Evidence] Security Footage Anomaly: On the security panel by the door. The log is corrupted from 22:00 to 22:15, the time of death. This is an automatic find.
- [Evidence] Encrypted Comms Log: Hidden inside a false bottom of a desk drawer to the left of the main terminal. You must activate your scanner's EM view to see the hidden compartment's outline.
- [Evidence] Aethelred Biotics Internal Memo: Pinned to a corkboard behind a plant. It details budget cuts to Thorne's department, signed by Director Valerius.
Unlocking Thorne's Encrypted Terminal
The final step in the lab is accessing Thorne's computer. The password is a logic puzzle based on his research notes scattered around the monitor. The clues point to atomic numbers of elements mentioned in his project notes: Osmium (76), Iridium (77), and Platinum (78). The password is 767778. Accessing the terminal grants you [Evidence] Project Seraphim Files, revealing the victim was working on a dangerous biological agent.
The Aethelred Biotics Server Room Puzzle
Your next lead points to the corporate server room to find out who accessed the Seraphim files. The room is locked down, requiring you to solve a coolant-flow logic puzzle to prevent a system-wide security alert.
Infographic showing the server room puzzle solution for the Forensic M.E. Protocol Case 3 walkthrough.
Finding the Maintenance Keycard
The server room door is sealed. To get in, you need the Maintenance Keycard. It's not in the server room itself. Head back to the main lobby and speak to the receptionist droid. If you present the Aethelred Biotics Internal Memo, the droid will complain about budget cuts leading to lax security protocols and mention a master keycard being stored in the first-floor janitorial closet. The closet is just past the lobby restrooms; the keycard is on a hook inside.
Re-routing the Coolant Flow (The Logic Grid)
Inside the server room, the main console is inaccessible due to a thermal lockdown. You must use the coolant control panel to divert flow to the mainframe core. This is a hexagonal grid puzzle. The goal is to create an unbroken path from the blue input node (A-1) to the red output node (F-5).
The solution requires you to rotate the hexagonal tiles to connect the pipes. The most efficient path is A-1 → B-2 → C-2 → C-3 → D-4 → E-4 → F-5. Completing this puzzle grants you access to the main server terminal without triggering the alarm, which is a requirement for the 'Ghost in the Machine' achievement.
Decrypting the Executive Email Server
With the server accessible, you can now search the email archives. You're looking for any communication regarding "Project Seraphim." A search filter will reveal a heavily encrypted email chain between an external account and an internal executive. You cannot decrypt it yet, but downloading the raw data gives you [Evidence] Encrypted Executive Correspondence. This is a crucial piece of evidence for the final confrontation.
Tracking Down the Three Cipher Keys
Dr. Thorne's terminal mentioned a failsafe: a data vault containing the unredacted truth about Project Seraphim. The vault requires three unique cryptographic keys, which he hid in three separate locations around the Aethelred Biotics headquarters.
Key #1: The Greenhouse Anomaly
The first key is in the rooftop greenhouse. Thorne's notes mention his favorite plant, a rare lunar orchid. Use your scanner on the orchids in the central planter. One of them will show an anomalous energy signature. Interacting with it reveals a small, hidden compartment in the planter's base containing the [Key Item] Seraphim Key Alpha.
Key #2: The Executive Suite Safe
Director Valerius's office contains a large, ornate safe behind a painting of the Aethelred tower. The combination is tied to the company's founding. Check the corporate history plaque in the main lobby. It mentions the founding year (2077) and the number of original board members (5). The code is the year followed by the number of members: 20775. Inside the safe, you'll find [Evidence] Unsigned Contract with a Rival Corp and the [Key Item] Seraphim Key Beta.
Key #3: Reconstructing the Shattered Datapad
This is the most complex step. Return to your forensic lab and use the evidence analyzer on the Shattered Datapad you found in Thorne's lab. This initiates a reconstruction mini-game where you must piece the fragments together.
Annotated diagram explaining how to reconstruct the shattered datapad.
The key is to ignore the image on the screen and focus on the electronic traces on the fragments. Align the main power conduit trace that runs from the top left corner to the bottom right. Once the main power line is complete, the smaller fragments will snap into place much easier. A correctly assembled datapad reveals a final audio log from Thorne, which gives you [Evidence] Thorne's Final Confession and the [Key Item] Seraphim Key Gamma.
Confronting the Suspects
With all three keys, you can open Thorne's data vault, located in the R&D wing's cold storage. Inside, you find the complete, unredacted [Evidence] Unredacted Seraphim Data, which proves the project was designed as a weapon and that someone was leaking the data to a rival corporation. Now you have everything you need to confront the two main suspects: Director Valerius and Lead Scientist Kaito.
Comic grid showing the final accusation scene with Valerius and Kaito.
Presenting Evidence to Director Valerius
First, confront Director Valerius in his office. Presenting him with the evidence will elicit denials and threats. The key pieces to present are:
- Unsigned Contract with a Rival Corp: He will claim it was a potential merger, not espionage.
- Aethelred Biotics Internal Memo: He will dismiss it as standard corporate governance.
- Unredacted Seraphim Data: He will express shock and blame Thorne for going rogue.
His deflections are important. Do not accuse him yet. Exhaust all dialogue and evidence options first.
The Cross-Examination of Lead Scientist Kaito
Next, find Kaito in the main R&D lab. He is nervous and defensive. He was Thorne's rival but claims to be innocent. The key is to present the Encrypted Comms Log. Your system will finally be able to decrypt it, revealing it's Kaito's personal log. It shows he knew Thorne was going to expose the project and tried to talk him out of it, fearing for their safety. He is not the mole.
The Final Accusation: Unmasking the Mole
Return to Director Valerius's office, where Kaito will also be present. This is the final confrontation. When prompted to make an accusation, choose Director Valerius. The game will prompt you for the definitive piece of evidence that proves he is the killer and the mole.
The correct choice is the Encrypted Executive Correspondence. Your system, having analyzed Kaito's lighter encryption, can now perform a comparative analysis and break the heavier encryption on the executive emails. The decrypted messages show Valerius communicating with the rival corporation, planning to murder Thorne and sell them the Seraphim data. This is the checkmate.
How to Get the True Ending (S-Rank)
Achieving the S-rank in Case 3 is not just about picking the right culprit. It requires a perfect run with all evidence collected and no mistakes during key sequences. If you miss any steps, you may get the Neutral Ending (Valerius is arrested, but the conspiracy is covered up) or the Bad Ending (you accuse the wrong person).
Poster celebrating the S-Rank True Ending requirements for Case 3.
Here is a definitive checklist for the S-Rank True Ending:
- Collect All 12 Pieces of Evidence: You must have every single piece of evidence listed in this guide before the final confrontation.
- Don't Trigger the Server Room Alarm: Successfully solve the coolant grid puzzle on your first attempt.
- Present All Key Evidence to Both Suspects: You must exhaust all dialogue and evidence presentation options with both Valerius and Kaito before making a final accusation.
- Correctly Identify the Killer: Accuse Director Valerius.
- Present the Correct Final Evidence: Use the Encrypted Executive Correspondence as your final proof.
Following these steps results in Valerius's arrest, Kaito taking over the department to decommission Project Seraphim safely, and Aethelred Biotics's illegal activities being fully exposed to the public. You'll be rewarded with the S-rank, the 'Seraphim Silenced' achievement, and a higher score for the chapter.
Frequently Asked Questions about Case 3
Q: Where is the last piece of evidence in Thorne's lab? A: The most commonly missed piece is the Encrypted Comms Log. It's in a hidden compartment in the desk drawer to the left of his terminal. You must use your scanner's electromagnetic (EM) view mode to see its outline.
Q: What's the code for the Executive Suite safe? A: The code is 20775. It's derived from Aethelred's founding year (2077) and the number of original board members (5), both mentioned on a plaque in the building's main lobby.
Q: Can you complete the case without accusing Valerius? A: You can accuse Lead Scientist Kaito, but this leads to the Bad Ending. Kaito will be arrested, Valerius will go free, and you will receive a low case score and a reprimand from your superiors for presenting a weak case.
Q: How do I get the 'Ghost in the Machine' achievement in Case 3? A: This achievement is awarded for accessing the Aethelred server room and downloading the encrypted emails without triggering the security alarm. This means solving the coolant flow logic grid puzzle correctly on your first try.