Temporarily disable ship (either via hacking database, overloading generators, or otherwise stopping it without ruining it forever), commandeer said ship, and immobilize Zymandis crew (as much is possible, fighting back against dissenters if necessary). Question whatever crew is left after the ship is overtaken to see who is willing to defect to the ALASTAIR side, who has information, and who will need to remain imprisoned.

Keep the ship, keep the prisoners! Bring it and their version of timeline.exe back to Oska for study.