Atomic Heart is a game about the illusion of choice. This could be why placing map markers is up in the air. This includes the choice when it comes to the ending. Here are all endings in Atomic Heart and how to get them.
How many endings does Atomic Heart have?
There are two endings for Atomic Heart. Don't worry about some random choice or series of decisions deciding the ending either. It all comes down to a simple choice right at the end. P-3 can either give up the fight and leave Facility 3826 or continue with the initial plan of confronting Sechenov.
Related: How to unlock all Polygon Testing Grounds in Atomic Heart
If the player chooses the first option, P-3 will destroy the "AI" Charles and disappear from Facility 3826. This allows Sechenov to activate Kollektiv 2.0. Another scene will show that Charles actually survived and manages to escape as a living mass of Polymer.
The second option has P-3 asking his mother-in-law, Granny Zina, to show him her arsenal. P-3 will then tear through Sechenov's bodyguards to then mortally wound the scientist. Sechenov tells P-3 that Charles has been manipulating P-3 throughout the entirety of the game. Charles confirms this and explains he was the one causing P-3 to black out and used him to murder Molotov and Filatova. The "AI" planned to kill Sechenov and take control of the Neuro-Polymer project so he could eliminate humanity and institute a new species of Polymer life forms. Charles then knocks out P-3, steals the Neuro-Polymer, puts an end to Sechenov, and finally disappears. P-3 is left in a coma where he has visions of his deceased wife.
For more Atomic Heart goodies, check out How to fix stuttering and performance issues in Atomic Heart on Pro Game Guides.