Ultimate Guide to Playing and Transcoding Downloaded Videos
Wrangling Subtitles
Before we dive into how to manipulate subtitles, it's important to familiarize yourself with the different types of subtitles you're likely to run into, as well as some of the nomenclature.

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Hard: Also known as open subtitles, hard subs describe text that is merged right into the original video frames and can't be undone. The advantage to using hard subs is that it doesn't require any special equipment or playback software. The biggest drawback is that viewers can never turn them off.
Soft: Also known as closed subtitles, softsubs differ from hard subs in that these are separate, specially marked up text. Unlike hard subs, softsubs requires player support. The main advantages to softsubs are that they can be turned off and they can be edited.
SubRip (.srt): Strictly a text-based subtitle, SRT subtitles are also one of the most popular text-based formats. SRT subtitles are widely supported by both a variety of players and subtitle creation programs.
SubStation Alpha (.ssa): Another text- based subtitle format, SSAs have been around a long time and are particularly popular in the anime community.
Advanced SubStation Alpha (.ass): Stop giggling at the file extension, there's nothing dirty about ASS subtitles (okay, you can giggle a little bit). As the name implies, these are a bit more advanced than standard SSA subtitles and are able to produce anything from simple texts to manual graphic editing, like what's used in karaoke.
SAMI (.smi): Short for Synchronized Accessible Media Interchange, SAMI subtitles were Microsoft's first attempt to create a captioning format for PC video files. SAMI is natively supported by Microsoft video players (WMP included), and are usually embedded in an ASF container.
Downloading Pre-Made Subtitles
There are a few different resources for downloading subtitles for everything from anime to movies, and everything in between. Some of these include:
How to Package Subtitles into MKV Files
To embed subtitles into MKV files without first converting the video to a mobile friendly format (such as MP4), download and install MKVToolnix, which you can grab from here

Click on the Add button and select your MKV video. Now click on the Add button a second time, but this time locate and select your subtitle file. Click on Browse to choose an output location and filename, then click on Start muxing.

Because you're not encoding and simply adding subtitles, the process doesn't take very long, even on slower systems. When it's finished, open up your video file and you should now see your subtitles.
Fix Syncing Issues, Edit Subtitles, and Create Your Own Text
Sometimes you'll run into subtitles that don't quite sync up correctly with the video you're watching. Even if the syncing is off just a couple of seconds, it can ruin the entire experience at worst, and at best, it will be a constant annoyance throughout the length of the film. Here's how you can fix a misaligned subtitle.

Downloand and install Aegisub from here. There are other programs that do the same thing, but we like Aegisub for its robust support, snappy performance, and intuitive interface. Once you have Aegisub up and running, open up the out-of-sync video file by clicking on Video>Open Video. Aegisub will display the video in the top half of the window and the subtitles in the bottom.

If the entire movie is out of sync, all you need to do is click on Timing>Shift Timing (or mash CTRL+1) and tell Aegisub to shift the subtitles in either direction. For example, if the subtitles start playing 3 seconds too soon, enter 0:03:00.00 in the Time field and select the Forward radio button and click OK. Also note that in addition to 'All rows,' you also have the option of shifting 'Selected rows' and 'Selection onward,' as well as whether to adjust both the start and end times, or one or the other only.

To fix a single subtitle that's out of whack, simply highlight the selection and then direct your attention to the top-right. You'll notice a start field and end field, both of which can be edited. Adjust the time so that you have the subtitle where you want it, then press the Commit button. You can also edit subtitles this way - just edit the text after you highlight the selection and press Commit when you're finished.

Creating your own subtitles is just as easy, albeit more time consuming. However, the effort won't be in vain if you have a knack for humor and decide to write your own script for a foreign film or anime. To create subtitles, open up a video as you did before, then click on Files>New Subtitles. Adjust the slider to any point in the movie you want to add text. Start typing in the text box, edit the start and end time, and press Commit. When you're finished, click on File>Save Subtitles.
Convert Soft Subtitles to Hard Subtitles
There's a good chance your mobile media player doesn't support soft subtitles, so to get around this, you'll need to convert them to hard subtitles, which are integrated right into the video itself. Here's how.
Download and install the 32-bit version of VirtualDub from here, even if you have a 64-bit system. Why? Because the 64-bit version does not support 32-bit codecs, which we're going to need. And don't worry, the 32-bit version of VirtualDub will work without a hitch on a 64-bit platform.

Next, download the VirtualDub Subtitler Plug-in from here and unpack the subtitler.vdf file to the same location as your video file. Open up VirtualDub and navigate to Video>Filters, or press CTRL+F. In the pop-up window that appears, click on Add>Load and select the subtitler.vdf file and click OK twice.

We don't want to say 'told you so,' but if you see the above error message, it means you ignored our previous step and downloaded the 64-bit version of VirtualDub anyway. Trust us, it just isn't going to work.

Before proceeding, we need to convert the subtitles to .ssa so that VirtualDub can read them. We can do this with DivXLand Media Subtitler, which you can dowload from here. Fire up the program, open up the .srt file, and save it as a SubStation Alpha file.

Now go back into VirtualDub and open up your video (File>Open Video). Next, navigate to Video>Filters and double-click on the filter you added earlier. Click the ... button in the Sub Station Alpha field, select the .ssa file you just converted, and click OK twice.

Finally, click on File>Save as AVI and sit back while VirtualDub works on your video.