Very few singular choices immediately impact the story and the end of the game. Most of them are a series of decisions, depending on who you align with.
Character Storylines & Lessons
Each Alter in the game has their own personal storyline and a Lesson they can teach Jan. This usually means going along with their requests to build certain modules and achieve certain tasks, as well as sometimes collecting their lost cargo on the map. Lessons unlock additional dialog options, and at least two must be unlocked for certain endings.
Tabula Rasa
At one point in the story, you will need to make a decision, during the mission Tabula Rasa. This is the most impactful decision in the game. At one point, some Alters will leave your base, depending on your choice. Some can return. However, if you go with Maxwell, The Technician will leave forever.
Ally Corporation
There are multiple paths to align with the Corporation, most of which center around siding with Agatha and using her suggestions when the time comes.
Maxwell
Maxwell has his own story tied to whether you choose to side with him over the corporation.
Lucas
Lucas can help at several key points throughout the game, but only if you keep building Rapidium Arks at a reasonable pace. You should have all 5 before you leave Act 2. Being on good terms with Lucas also unlocks Jan Refiner’s life lesson and storyline.
Lucas can be involved in multiple endings, if he is on your side. These can both align with either Maxwell or Lena
Lena
Your choices with Lena change her involvement in the story and also what happens to her at the end. There will be several opportunities throughout the game to either work with Lena or cut her off.
At the start of Act 3 Lena is told everything. If you have decided not to tell her about the Alters to this point, you will not have any positive relations going forward.
The Botanist
The Botanist has his own ending if you choose to let him speak with Lena and eventually take Jan’s place going back to Earth
The Scientist
The Scientist also has his own ending. If you make a choice that leaves the rebel base intact (so far, just siding with Maxwell for me) and complete The Scientists story, he will ask to stay on the planet.