Cancel the last ship command in Stellaris

Set their behaviour to passive.

You can change a fleets behaviour in the fleet window (bottom left), can't provide a screenshot right now, but should be easy to find.

There are three options:

• aggressive: fleet automatically attacks hostiles
• passive: fleet won't attack on its own, but will defend itself
• evasive: fleet retreats as soon as enemies appear.

non-combat ships are on evasive by default and as such they will run immediately, when a hostile is in the system. I recommend setting them to passive while exploring, but evasive, once you get in a war.

There is a Feature called Automatic Exploration that is unlocked by the Physics Technology Automated Exploration Protocols. This will allow your Science Ships to explore the galaxy while controlled by AI (though it will still need a scientist, as I recall). It also increases your surveying speed by 25%.

The only prerequisite for this technology to appear in your Physics tech choices is that the current game year be 2210 or later. Here is what it looks like in-game: