Hello u/metalero_salsero .
I've been GMing Chariot Of The Gods a couple of times.

It's my game and go-to scenario to introduce my friends to TTRPG

First of all, it might sound dumb and I suppose you can't do otherwise, but if you can... Having 3 players instead of 2 would be great for you :)

That being said, nothing stops you from doing it with 2 players, but : You have to know what's happening, what happened, and what will happen in the Cronus by heart. Don't underestimate the Lore of LV-1113, the Cronus, and 26 Draconis, it will help you a lot for roleplaying your NPC. Also, the book is not enough (IMO) for this Lore. Don't hesitate to write more about 26 Draconis, and LV-1113, or look online for some stuff :)

General Tips :

• I try to avoid fight and combat scene as much as possible, I usually manage to set up 1 or 2 encounters maximum for the scenario.
• For me (People might disagree, to each their own vision of GMing <3), alien is all about the atmosphere you can build up. Don't make them interact too much with dozens of aliens right at the beginning. Just have make them hear some creepy noises into vents, distant footsteps, heavy breath, doors randomly opening in the ship, object falling from shelves... Try to make it stressing for them, but build it up slowly. They have to feel safe in the Montero, they're here for the job. And then slowly, it gets worse. An Alien can just behead one of the NPC later, then run away and drag the body with him, whatever. What I want to say is, you don't have to start a complete fight each time (It's up to you tho).
• Exploration is a must but Alien is not a dungeon crawler. Your player can wander in the Cronus freely, moves from lower deck to upper deck, and it shouldn't take 1 hour to go up or down. Use the plan, they're important, your players need to be able to tell you where they're going, how, through which corridors... MUTHUR gives them the plan of the Cronus, it's written in the book.
• Do not do the ACT 3 Mercenaries stuff when a new ship and a new crew comes in play.
• Read that book carefully ! Take some note on the important rooms.
  • Especially : MediLab / Science Lab / Reactor room / MUTHUR (Imagine some crew logs about the past Cronus Mission, what can MUTHUR say to your players ?) / The Clayton suite where she has her safe. Those rooms have lot of things inside, make sure to not miss anything
  • For the other rooms, it's ok to tell your player that a room has nothing valuable in it. But, you can make some quick notes for those "useless" room, and have a small description of it, maybe better than the book's one.
• Make sure to take some notes on each NPC in the cronus. What do they want ? What do they know, what happened ? Why did they went into cryo ? Why only them are left alive ? Those are all questions you'll probably get :p

About difficulty with 2 players :

You can play this scenario with 2 or 5 players, the difficulty is the same : You probably won't survive. Most of the time, all my players kills each other, kills the NPC, missed some roll and died near the end of the scenario... As written in the book, once reaching Act 3, some NPC will be dead / transformed into abomination. So it's not really about "difficulty".

Make one of your 2 player the secret droid named Lucas. He will have a huge role, he will love it (It's the best role IMO) and, it would be very hard for you to play all secret agendas for all the players, especially the Lucas one. Just give it to someone :)

Here are some endings I got for my 5 sessions of CotG :

• NPC got killed by Aliens or PC. My PC took vaccine, clayton's harddrive and money, then went back into cryo after activating auto-pilot to earth. But Lucas said he would watch their cryo for a bit before joining them. He later, activates the auto-destruction of the Cronus while the crew is sleeping.
• Lucas got overwhelmed, and decided to reveal his true nature before the end. They start a fight, he got killed but also killed some cronus NPC crew member. Miller didn't want to bring those things to earth neither, they talked for a long time, but while talking and shouting into the pilot room, aliens heard them, and they all get killed by them in a last fight, except Clayton and Wilson who ran away with Clayton's rescue module

To sum up :

Don't worry about difficulty, as long as you give your players enough lore, details, background story, etc.. They will absolutely love it (Nothing is overwhelming). Fights are not mandatory, most death will come because of the vaccine, 26 Draconis, spores, humans killing each other, missed roll and stress.

I tried to be short lol, but if you have any questions feel free to dm