Holdover

A young girl named Marie wakes up in a dank, dark laboratory wearing nothing but a gray, one-piece swimsuit, and two metal anklets around her bare feet, designed to keep her healthy. A holographic message from her father says that she should have just woken up from a special chamber designed to cure an illness of hers, and that she should now try to leave the facility she resides in.

Easier said than done, of course, since the facility has long since been abandoned, is nearly completely flooded (and despite being suited for it, those anklets make it impossible to swim), and is full of various security robots out to vaporize her (and her swimsuit) with powerful lasers. She quickly finds an advanced armor swimsuit that can shield her from the lasers, at the cost of vaporizing the half that was hit.

Thus goes Holdover, a surprisingly good timing-based platformer, with plenty of girl-running-around-completely-naked action. Find it here.

Tropes used in Holdover include:

Barbie Doll Anatomy- Marie's sprite when the swimsuit is destroyed.
Bonus Material - In addition of the suggestive picture mentioned below, another picture with little fanservice appears in the game's folder when you access a secret machine at the left of your starting room after collecting all blue hearts and the arm grab ability.
Blessed with Suck - You know, for devices intended to keep Marie alive, those heavy, buoyancy-killing computer anklets sure end up killing her a lot in the now-flooded installation.
Clothing Damage - Initially, you can only take one hit, which will vaporize your gray swimsuit and leave you naked (and dead). The first upgrade obtained upgrades your swimsuit, letting it take the damage instead of you, at the cost of that half getting vaporized. Marie proceeds to run around topless, bottomless or completely naked, seemingly without giving a care. This is actually a deliberate part of the gameplay - Marie will often have to let the swimsuit take a hit for her so she can run past various obstacles with the only loss being her dignity. As such, as fun as it is, running around naked can be counter-productive.
- As a bonus, the image of Marie that shows up whenever she speaks also reflects her current clothing status. Even the ending image changes depending on whether she still had a swimsuit or burst out of the facility in the buff, although the ending itself remains the same.
Everything Trying to Kill You - not as bad as, say, I Wanna Be the Guy, but the walls are lined with spikes, and there are security robots all over the place which will be more than glad to vaporize you with a quick laser beam. You don't ever get a way to fight back, either, so you're forced to sneak around pretty much everything in the entire game.
- That's justified. You really are the little girl, with no weapons of any sort.
Fan Service - Marie's wearing a skin-tight leotard that will come apart in pieces, runs through sections of the game half or completely naked, with her portrait reflecting her state of (un)dress. Yeah.
- And upon winning, a very suggestive picture of her will appear in the game's folder as a reward.
Girlish Pigtails
Good Bad Translation

"Do you overwrite?"
"Do you return to title?"

100% Completion - Getting all the blue hearts yields a bonus picture.
Let's Play - a decent one by ShoMakahari
Lost Forever - after the SOS signal is sent, the game goes on, but if you left any blue hearts in other rooms, you won't be able to get them back. Also, if you predict that you might not be able to get the hearts back, you may save on a new slot next to the machine that sends the signal. However, due to a glitch, when you load a save, if you're near a sign or machine, the game will automatically read it/use it. This means that if you saved next to the final machine, the Point of No Return will be triggered when the game is loaded.
Malevolent Architecture - ...why are there rows of giant spikes in a research installation, again?
Metroidvania
One-Hit-Point Wonder - Initially played completely straight, but tossed out the window when you get the upgraded suit. Running around naked leaves you as one of these, however. Unsurprisingly played straight in the shooter segment.
Oxygen Meter - The main feature of the game. Getting blue hearts helps upgrade it.
Point of No Return - after the Unexpected Shmup Level, you can't go back to most rooms.
Save Scumming - the game makes sure to point out the quicksave functionality. Which is good, because you're going to need it; you will die. A lot. (It even leaves a permanent splat of blood wherever you died, so you can keep track of where you messed up!)
Stripperiffic - somehow a swimsuit is supposed to qualify for armor. A swimsuit that gives way at the slightest bit of damage, leaving the user completely naked. Yeaaaaaaah.
Unexpected Shmup Level - After sending out the SOS, and being given some grim dialog suggesting a Shoot the Shaggy Dog ending... it gets picked up by two jet fighters who were coincidentally in the area. You then have to shoot down 70 blimps which apparently disrupts the SOS signal sent by Marie before the game gets back on track.