During your gameplay, you will have to conduct a scratch marks analysis in Spider-Man 2 during the game’s tenth mission. This analysis is essentially a puzzle that needs to be solved before you can progress to the next step of the story.
Warning: Some gameplay and story spoilers ahead.
You will have to conduct this analysis during the ‘Make Your Own Choices’ mission of the game’s main storyline. In this mission, you will take on the role of Miles Morales, who has been tasked with finding the location of Felicia Hardy aka Black Cat, in order to warn her about Kraven’s intention of hunting her down. Upon completing this mission, you will gain 2000 XP as a reward.
On This Page
How To Start The ‘Make Your Own Choices’ Mission
After you complete the ninth main story mission ‘Bad Guys on the Block’, Miles will receive a call from MJ, asking him to convene at a location in Midtown. Once you reach the waypoint (a rooftop of a building in Midtown), the mission will begin.
Once you reach the rooftop, hold L2 in order to scan the environment and begin your investigation. Eventually, you will come across several scratch marks on a sunbed lying on the rooftop. This is where you will need to begin your scratch marks analysis.
How To Complete The Spider-Man 2 Scratch Marks Analysis
The scratch mark analysis in Spider-Man 2 is basically a puzzle-based mini-game. Your task is to clear out the corrupted atoms from the molecules present in the scratch marks, without destroying any of the essential atoms. The mini-game is split into three distinct stages. In all of them, you will be presented with different types of molecules and you will have to carefully separate and destroy the corrupt atoms.
In this mini-game, corrupted atoms will be marked red, resembling a spiked ball, similar to mines in Minefield. The essential atoms will be marked in green.
Stage One
In the first stage of scratch marks analysis in Spider-Man 2, you will have to destroy eight corrupted atoms. The molecule presented to you will house a total of 12 atoms, among which four are essential and eight are corrupted. To destroy a corrupted atom, you will need to select the desired atom with the left stick and hit the X button to destroy it.
In the first stage, you can begin by destroying the corrupt atom housed at the bottom of the left side of the molecule.

After that, proceed to destroy this corrupted atom, housed in the bottom of the right side of the molecule to complete the stage.

After this, the molecule will stabilize and you can move on to the next stage.
Also Read: Best Skills To Unlock First In Marvel’s Spider-Man 2
Stage Two
Stage two of the Spider-Man 2 scratch marks analysis mini-game offers a little more challenge than the first part. In this stage, the presented molecule will have neutral atoms, along with corrupted and essential atoms. The molecule presented in stage two of the analysis includes a total of 14 atoms, among which four are corrupt, five are neutral, and five are essential.
Neutral atoms will be marked in orange color and can be destroyed without compromising the integrity of the molecule. Furthermore, strategically destroying a neutral atom will also destroy the connected corrupt atoms. However, destroying the wrong neutral atom can lead to the destruction of essential atoms in the molecule.
To get started, you can destroy this neutral atom on the left side of the molecule first.

After that, destroy this neutral atom on the lower side of the molecule.

Finally, destroy the last remaining neutral atom on the right side of the molecule to finish the stage.

Stage Three
The final and most difficult part of the scratch marks analysis puzzle will require you to destroy four corrupted atoms. This molecule is a complex one and you will have to rotate the molecule structure with the right stick in order to properly assess the locations and connections of neutral and corrupted atoms.
To start, rotate the molecule to the right, find and destroy the following neutral atom.

After that, rotate the molecule even further and delete the following neutral atom.

Finally, completely rotate the molecule once again in order to delete the final neutral atom, which will clear out the corruption.

Once you complete all three stages of the scratch marks analysis in Spider-Man 2, you can proceed with the ‘Make Your Own Choices’ mission that includes a thrilling chase, where you follow the Black Cat through a series of portals.