How do I hijack an Atlas?

Solution 1:

If it blows up you damaged the Atlas too much. You need to both shatter the cockpit and kill the pilot, you'll see no prompt to hijack it before you kill the pilot.

I'd try to kill the pilot with a lower damage weapon, to avoid blowing up the mech at that point. An upgraded high-damage sniper rifle might deal to much damage at once for this to work.

Solution 2:

I found that with 3 shots with the black widow V with pierce IV and extended barrel IV while under adrenaline rush will kill the pilot and shatter the glass and only drop about 1/12th of the mechs health. (this is all after the shields have been dropped)

Solution 3:

You need to use the Graal Spike Thrower V. Make sure you aim for the cockpit. I shot it about 4 times after the shields were down.