Cloning Players In Adobe After Effects
Record your video with your actor(s) doing whatever the script calls for, Move them to a different spot to act as the "clone" and record it as many times as you want.. Do not put them to close together, You must keep them seperated or they will be cut off during editing. (Tutorial video shot in campaign but works with multiplayer too of course)
source video
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Now open After Effects
First you will need to create a new composition,So open After effects,Create a New Project. And make new new composition

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These settings should be ideal for machinima video; adjust the Duration option to give yourself enough time on the timeline for your video.

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Import your file(s)

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Drag the video(s) onto the timeline

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Trim the video using the handles(1).If you shot the video all in one clip then Trim your video to each clone scene,and your background scene.(continued)

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Trim a scene and copy and paste the video and re-trim the next clone as many times as needed(depends on how many clones you have) Like this....the bottom clip is my background, The other 2 clips are each spartan I am cloning (seen in the source video above)
Background Video

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Here is clone 1

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Here is clone 2

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Align the clips(1), make sure the background scene is on the bottom. Also, Trim the work area to Emcompass your clip(2).
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right click the first 2 clips and create a new mask for them(no not apply a mask on the background clip)

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Expand the options by clicking the little triangles. now select "Mask Expansion"

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Drag the small squares around your clone

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Like this,notice how the second clip now shows,a mask elimiates all video outside of the yellow line.The background clip is also showing around clip one if you notice.

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Create a mask for each clone you have and move the yellow square as needed for each one.
Now to export your clip. Click Composition>Add to render Queue

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Adjust your settings by clicking the blue text,and set the output directory to Desktop or whatever folder you want. Then Click the Render button.

Final outcome