As of today, this achievement is still bugged, but I have a workaround to getting it.
Enable Dev Mode From the Main Menu
(For me dev mode was bugged somehow and it only worked by restarting and turning it on from the main menu, what is Stress Level Zero doing over there????)
Click on Mods < Settings < Enable Dev Mode
Enter the first level, go further in, spawn Apollo
Instead, open up your menu, select DevTools, and then two tools should spawn.
Grab the blue tool, open up your menu again, then select Utilities.
From the list on the right “Apollo” should be there but if it’s not, use the down arrow on the left side till you see the category “Toy” then select that and it should be there.
Then spawn Apollo with the tool.
Proceed through the campaign
After you finish Descent the game will take you to your last save in the 02 Hub. Don’t worry about it and spawn Apollo again, then head through the Quarantine door and continue on.
There are a few other instances where Apollo doesn’t show up at the start of the level, so just spawn it again and keep going.
If you happen to die by falling and lose Apollo just restart the mission and spawn him again.
Once you reach the end and manage to climb up the windmill with only one hand available (using the tall avatar is easiest) the achievement won’t unlock, but assuming that you did everything legit and carried Apollo the entire way, then I would consider the achievement unlocked. Since the devs haven’t fixed it yet, we only need one last workaround.
Download Steam Achievement Manager
Search up steam achievement manager and click the first link from github.
Scroll down till you see “download latest release”, click that, and then click and download SteamAchievementManager-7.0.25.zip
Open the file and launch “SAM.Game.exe”
Scroll till you find Bonelab from the list and select it
Find the My Pal Apollo achievement, hit the check box on the left, then “Commit Changes” at the top right. Congrats!
Assuming you did everything legit and carried Apollo through all levels from start to finish, then it is fair for you to unlock this achievement. It’s only fair to use the achievement manager for stuff that is bugged. I’ve only had to do this one other time, which was for collecting all the rings in Dark Souls 3. If the devs won’t fix it, we will.