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[COMPLETED] Thomas is stiles, in the Pack's eyes he was only kidnapped a month, what they didn't know is that stiles, and about 100 other kids from the Pack's earth were taken to the Scorched earth.
There were even more kids in the scorched earth but when they went there their lives completely restarted, from when they were born till a month after they were taken. All the survivors ended up finding a way to the safe haven, which happened to be on the Pack's earth. The FBI found them and split them all up.