This is a review for the first book in the Rho Agenda series by Richard Phillips.
I've stopped reading this after the first ~20% of the book, so the following may contain spoilers from up to then. That said, in my opinion most the story is so predictable that reading this is really not going to ruin anything for you.
So, what happens? Well, the book starts with a just-graduated postdoc setting up an experiment on a crashed ufo. Apparently a bunch of really clever scientist has been working on the ship for a few years, but they never managed to even scratch its surface, let alone getting it open. So now it's sitting all alone in a hangar, and a single scientist can mess with it as he pleases.
Now, the freshly baked Dr. has an incredibly clever idea. Apparently back then eyewitnesses noticed a blue glow around the crashing ship, which could only be caused by Cherenkov radiation (we'll just buy that for now), but our Dr. can see no possible source of such radiation. Obviously, he concludes, Cherenkov radiation is going to have some effect on the ship. So he sets up a little particle accelerator ring and directs a small beam of such radiation on the ship. Lo and behold, the ship opens(!). Up to this point the story isn't actually quite as bad as it sounds. You could probably look over the fact a single postdoc working alone on an alien ship is rather unlikely and discard the missing connection between an observed blue glow during flight and an opening mechanism. However, from this point on the book actually started to make me agitated.
What happens next is that our ingenious scientist, being alone in a hangar, doesn't tell anyone anything, but just walks into the ship. The fact that e.g. it may close just as randomly as it opened doesn't even occur to him. Of course, something bad happens and turns the Dr. into a really clever bad guy who goes on to win 3 Nobel prizes before he is 30.
With this backstory, the book goes to the present where three teenagers and a drug addict (separately) find a second alien ship somewhere in a cave in New Mexico. They're teenagers and drug addicts, so them entering the ship through a hole (that was apparently shot by the first ship) without telling anyone is half-way reasonable. It becomes less plausible when they start putting some weird alien headsets on, which cause them a lot of pain and give them something like a memory dump of the second ship chasing the first ship and both ships crashing into earth. The drug addict concludes that the first ship is obviously an evil ship from the devil, the second ship sent by god, and the headsets meant for the 4 apocalytic riders (of which he is the first). (I don't know if that is just a random interlude or if this guy or his ideas are going to become important again later on).
The teenagers, on the other hand, conclude from this obviously trustworthy source of knowledge (who wouldn't take everything that and alien device dumps into your memory at face value) that they should not tell anyone about the ship (because "it would be bad if the same people who work on the first ship would investigate this one as well"). Instead, they decide to keep exploring it on their own (but what the want to achieve with that doesn't become clear). It then turns out the alien headsets gave them photographic memory and really good motoric skills, but that unfortunately gets them into trouble when they all quote the same passage from a book in a school exam. This delays their further exploring of the ship.
Meanwhile, the clever scientist from the beginning has made it to laboratory head and is up to something nasty. When an auditor reviews the files on his computer (of course, alone and after work hours), he shows up and tricks her into coming with him into a secret room in the ufo -- the trick being that he tells her that he'll show her even more of the bad things he's been up to. Having just realized how obvously scheming this guy actually is, the auditor does not hesitate at all to enter a secret room alone with the person for whose guilt she just found evidence. Dr. evil then gives her a good punch and an injection, which apparently turns her into his puppet.
At this point I stopped reading.