Errand of Mercy: Sentinel Statue
Immediately to your left upon starting the chapter is a statue you can scan.
Errand of Mercy: Grand Chest
Just past the statue, the path splits. Head up the slope to spot a large chest you can also scan.
Errand of Mercy: Golem Statue
And just past the chest is another large statue ready for scanning.
Errand of Mercy: Companion Statue
Continue just a little further to spot a campsite under the overarching rock. A fourth and final statue can be scanned here.
Where No Man Has Gone Before: The Lymax (Part 1 of 3)
Just after clearing the invisible Gorn Scouts, you'll round the bend to a bridge that needs extending. In the grass nearby is a Lymax corpse you can scan.
Where No Man Has Gone Before: The Lymax (Part 2 of 3)
When you reach the security center, you'll have head into the tunnel below to disable the coolant system. Do so, and head just past the first power cell to find a Lymax in a cage. He can be scanned.
Where No Man Has Gone Before: The Lymax (Part 3 of 3)
Now head to the very back of the security center. You'll find an ammo station and another Lymax floating in a tank. The tank can also be scanned.
The Apple Part 1: Glowflower
After swimming through the first tunnel, you'll squeeze through a narrow passageway in the rock. Immediately on the other side, you'll find this vine ready fro scanning.
The Apple Part 1: Water Cabbage
Just past the glowflower is another tunnel you'll need to swim through. Once you dive in, swim to the bottom to find these plants that can be scanned below.
The Apple Part 1: Stalactites
After swimming through the second, longer water tunnel, you'll surface near some large stalactites. These can be scanned.
The Apple Part 1: Crystal Formation
Shortly after you encounter the dogs, you'll scale a tall rock wall and reach a large chasm (you'll know you're there when Kirk wonders aloud if they can cross it). The rock formation directly in front of your entrance can be scanned.
The Apple Part 2: Instruments of Science? (1 of 3)
After Kirk sees the enslaved Lymax, you'll cross a thin bridge. Once across, head up the next flight of stairs and turn right. This lies atop a crate in the back of the area.
The Apple Part 2: Instruments of Science? (2 of 3)
Extend the bridge in front of the doorway nearby and cross. In the back of this small area, you'll find another instrument.
The Apple Part 2: Instruments of Science? (3 of 3)
Make your way toward complex until you reach a turret guarding the entrance. Move past it to find this next research item atop a crate.
The Apple Part 2: Tribble #5
Near the last instrument is a teleporter. Use it to reach a high ledge with some flame jets. Pass them or hack them to reach a small alcove where this little guy is hiding.
The Apple Part 2: Daniels' Audio Log #7
Once you enter the complex proper, hack the door straight ahead to unlock it. Enter the room beyond and look left to find this next to a chest.
The Apple Part 3: Instruments of Pain (1 of 2)
When you reach the prison section, you'll have two objective markers. Head to the one straight ahead. Look left in this holding cell to find this tool next to a Lymax corpse.
The Apple Part 3: Crewmember Audio Log
Now head to the second marker. In this cell, you'll find an audio log in the hands of a dead crew member.
The Apple Part 3: Daniels' Audio Log #8
You'll then be given a new marker. Follow it, but head straight instead of turning left at the fork. Hack the door and enter. Turn right to find another audio log atop a crate.
The Apple Part 3: Instruments of Pain (2 of 2)
In the following area, you'll spot Commodore Daniels in a cell. There are two doors on the left side of the room that let you sneak to the other end. Head through those doors to find some crates. This instrument sits atop one of them.