Both are "right" (or almost right) in that they are okay (but not perfect) English, but they different meanings, so it depends what you want.
The first one is a command. You are telling someone to go investigate the properties of some set of things. You might use this if you are writing an exam that other people will do. It probably should be "Investigate
its microstructure and mechanical properties" if there is only one item to be investigated. "their" is plural.
The second is a statement, written in passive. This is the type of sentence one often finds in academic writing. You could just as well say (in active voice) "This paper investigates its microstructure and mechanical properties"., Or perhaps better
"This paper iinvestigates the microstructure and mechanical properties of a component developed using plastics"